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In the massive South Island lies Spring Hills, a close knit village inhabited by hedgehogs, Sonic, a young blue hedgehog, has a race with his childhood friend, Monty. Sonic tries to outrun him due to his remarkable speed, yet want to play fair after Monty blamed him many times of cheating. As the race gets on the way, they both get interrupted by Elder Sage. Sage tells Monty that he needs to speak with Sonic alone. With the race postponed, Monty tells Sonic that they will continue their race fairly. Sonic soon walks with Sage towards the Great Hall of Hedgehogs.
Entering the Great Hall, Sage tells Sonic about previous "guardians" who have sworn to protect their Hedgehog clan from outside forces. Sage then informs Sonic about his father, Serio. Sage mentioned that not only Serio was a great friend, but was one of the guardians. Sonic tells Sage that his father never told him he was one of those protectors; he held his job private unlike taking care of his family. Sage tells Sonic that he still regrets letting Serio go in that fire five years ago that soon took his life. Sonic still upset about that runs off. Sage looks disappointed and forgets to tell Sonic that there was a reason he brought him here.
Unbeknownst to the hedgehogs, nearby miles away an army of robots commanded by E-100 Alpha talking in its computer voice to an unknown figure in its screen. The cloaked figure tells his commander bot to attack. E-100 then turns around and informs his other bots to attack. They soon march off while others rocket off towards Spring Hill. Back in Spring Hill, Sonic still upset about what happened back with Sage, he meets up with Amy. Amy tells Sonic about that date he promised; Sonic regrets it, but tells her next time. As he heads off, Amy yells to Sonic that he always promises. Sonic then meets with Monty once again as Monty talks about the race again, Sage runs towards Sonic and tells him and everyone else "Watch out!" Soon the hedgehogs start noticing robots arriving. The robots led by E-100 then tells its robot brethren to fire; the robots soon begin firing. Most of the village is destroyed; the hedgehogs try to escape, but most of them are either caught or killed inside their homes. Sonic, Amy, Sage, and Monty try to escape but as they do E-100 and few robots come after them. Sage yells at Sonic to use his speed; Sonic agrees and uses his speed to defeat the robots except E-100, who then fires at Sage. Before Sonic can get there, Monty jumps in front of Sage taking the hit.
Sonic is horrified; Sage and Amy are soon captured by other robots. Sonic gets hit by E-100 and decides to let him live. Then E-100 commands his robot army to depart as their mission is complete. When they leave, Sonic wakes up to see the damage of his homeland. Shocked and angry, he then notices Monty. He runs to him as Monty dying tells Sonic about that unfinished race. He grabs Sonic's hand and tells Sonic to find out who did this. Sonic promises him that he will and tells him that they will finish that race; before he can agree, Monty dies. Sonic hugely upset over his friend's death, his hometown almost destroyed, and other hedgehogs like Amy and Sage abducted. Sonic suddenly thinks about why that robot let him live, but then looks at Monty. He begins to make that promise come true. He sprints off to go anywhere except here.
Hours later, E-100 and the other robots that survived. As most of the robots take their hostages including Amy and Sage to a mountain. E-100 arrives in a deep cavern where it then meets its master. The cloaked figure arrives and tells his commander is it a success. E-100 then looks at its master and informs only one is left. The figure is visibly upset and screams at its commander; he demands his commander to find that remaining hedgehog and bring him here. E-100 agrees and flies off.
Sonic still running soon stops as he notices a flying creature coming towards him. Feeling threaten, Sonic turns defensive but the figure arrives and its revealed it is a eagle. Sonic confused and the eagle figure tells Sonic that his name is Zugo and informs him he is a Watcher. Sonic unaware of its meaning, Zugo explains that a Watcher is a guide that protects the Power of the Centrum. Sonic still confused as Zugo continues telling the Centrum is the essence of everything; every creature has guardians, who not only protect their clan, but form together as a one collective to team up with a Watcher to protect the Centrum.
Zugo then mentions part of the Centrum resides in seven mystical stones known as the Chaos Emeralds. Zugo mentions centuries ago one watcher is given the right to keep an eye on the stones. By this time, he was chosen to be that protector. Sonic wonders what happened; Zugo tells him someone ruin the ceremony and split the stones separately across this land. Sonic wonders who did this, and then Zugo tells him that person is the same one who sent those robots to Sonic's home. Sonic then gets angry and tells him who. Zugo then tells him his name is "Eggman" as so what he heard. Sonic tells him where he is at so he can find him. Zugo then tells him that he cannot go after this Eggman for what he done. Sonic tells him why can't he; Sonic tells Zugo Eggman ruined his home, captured his people, and killed his best friend. Zugo tells Sonic the only way to beat Eggman is to find the stones Eggman is trying to seek after as well. Sonic wonders why he can't; Zugo can only say that is not part of his ethics to find what he lost, but Sonic is the right one. Zugo then flies off, but Sonic tells him where to go. Zugo then says, the stones will find you. Then Zugo leaves, Sonic unsure what he meant, but if this is only way to stop this Eggman, so be it.
Deep inside a mountainous area, the captured hedgehogs are held inside a energy-shield dome. Amy and others wonder where are they; Sage tells them that to stay calm. And then the cloaked figure arrives. Amy demands to know what is going on. The figure uncloaks himself to reveal to be the devious Eggman. The hedgehogs are stunned and Sage tells his captor why they are here. Eggman tells the elder to refer himself as Dr. Robotnik and that the reason they are here is because of in Robotnik's terms, "good use". Amy wonder what use; Robotnik only tells them is for him to know and they not; he then laughs manically and leaves. Amy wonders about the others, Sage soon tells her don't worry he knows "he will come." Amy looks confused. Sage winks and walks to the other captives consoling them. Amy still confused to what he said, but then thinks about one hedgehog that she knows is still alive. She then quietly mentions Sonic's name.
Across the region, Sonic using his amazing speed begins zipping the land as he bypasses Green Hill then Seaside Hill while knocking off little robots along the way. He then stops at Sandy Labyrinth, a deserted desert-landscape. Sonic treks carefully as he then senses a power. Not knowing what to expect, he hopes this is one of the stones. As he ventures to the area, he then gets attacked. Dodging the blasts, Sonic looks over to see E-100, the one responsible for killing Monty. E-100 attacks again; Sonic dodges and tries to speed away. E-100 begins chasing after him. As he speeds on, he then hears some sort flying noises like a helicopter. He then looks up to see someone coming towards him.
The figure is revealed to be a fox with flying tails. Sonic screams at his guest that robot is dangerous. The fox figure tells Sonic don't worry, he will distract the thing while Sonic continue what he is searching for. Sonic baffled. Noticing his new ally is giving him time, Sonic speeds back to the area to get back to what he was tracking; meanwhile, up in the sky, "Tails" tries to divert E-100 away from Sonic. E-100 begins firing at Tails, however, Tails dodges the blasts with his quick agility. Tails then flies towards an approaching sandstorm. E-100 chases after him, but as soon Tails enter the storm, E-100 gets caught in the swirling winds. With the flying dust blinding E-100's vision, Tails using his goggles escapes the storm and heads back to Sonic. E-100 still caught inside the sandstorm is unsure what to do next.
Sonic meanwhile looks towards a patch of sand and rocks. Sensing something is there, Sonic realizes one way to get down is use his speed. He soon jumps up and then rolls into a fast ball. As he spinning in a circular path, he then uses this motion to strike that layer of sand and rock. He makes a impact causing a dig-like path deep in the heavy sand and rocks where he then stops the motion. He soon sees a shining object; Sonic grabs it and decides to be like mole. He spins in a circular path again and uses his speed to create an alternate path to the surface. He jumps out to the sandy surface and looks at his hand to see the object. It is a yellow stone (shaped like a emerald); Tails then meets up with Sonic and notices the stone. Tails becomes ecstatic that finally one of the stones has been found. Sonic looks at Tails and tells him he know about this; Tails gives a short history that he and his fox clan have been intrigued about the Chaos Emeralds and remembered if all the stones combined it will become a powerful weapon.
Sonic looks a bit surprised that Zugo forgot about mentioning that tidbit. He then looks up at the sky and yells probably to Zugo and tell him that these stones become a weapon and that he lied to him. Tails mentioned that he learned this info from an Echidna known as Knuckles. Sonic pondered that maybe this Knuckles have info on where the other stones are at; he then tells Tails to bring him to Knuckles. Tails agree, he then tells Sonic to follow him. Sonic holding the yellow stone tight; he speeds off following Tails. As they venture away, E-100 begins to fly out of the sandstorm.
Back in the mountainous area to the Hedgehog's cage, Amy notices a robot keeping guard and wonders who it is. The robot seeing that she seems nice talks in its computer voice and telling her its name is E-123, part of the Omega squad. Amy wonders why it is being guard to themselves and not part of the big guy's army. E-123 explains to Amy that its program is to guard. Amy then gets an idea and tells E-123 that if its program is meant to guard, why not guard her to find help. E-123 tries to refuse, but Amy insists that it will make his maker proud and soon enough E-123 could be appointed leader. E-123 seems to like that and decides to let Amy get out of the cage. Sage and the others are stunned and worried about what that bot is going to do, but Amy tells them that she will be fine and that E-123 will protect her while she find Sonic and bring him back her to rescue the others. Sage agrees and tells her to be careful; she agrees. Amy and E-123 begin to head out before another robot arrives to spot them. It wants to know where they are going; E-123 tells the other bot that the maker wants her. The bot agrees and let them go; the bot soon takes over E-123's spot as guard. While, Amy and E-123 leaves; E-123 soon takes Amy and flies off the mountain.
Meantime, Tails brings Sonic to Necropolis. Sonic is amazed of this place and sees a lot of Echidnas and some of them worshiping. He wonders where is this Knuckles. Tails then sees Knuckles fighting off another Echidna. Tails and Sonic soon meet Knuckles, who informs Tails what is he doing here, but then sees Sonic. Knuckles is amazed seeing a hedgehog here in his homeland; Sonic soon gets emotional because of the lost of his home. Tails inform Knuckles about what he told him about the Chaos Emeralds. Knuckles tells him that if the stones fuse together it becomes a weapon. Unless it falls in the wrong hands, then the weapon could annihilate anything. Sonic wonders how he knows about this. Knuckles tells him it is part of the teachings from the Mitre—to whom Knuckles tell them it is the spiritual leader. He soon tells them that the Mitre and the Echidna Council are continuing to rebuild their home after a year ago, a group of anarchist echidnas known as a Dark Legion tried to take over the city. Sonic soon tells him that his home, Spring Hills, was destroyed by a group of robots led by and then Knuckles said Eggman. Sonic is stunned as Knuckles tells him the Dark Legion was using robots to aid their takeover and someone mentioned they got those bots from Eggman. Sonic soon tells him that he wants to go after the madman, but needs to continue his quest to find the stones.
Tails tell Knuckles, Sonic found one. Sonic shows the yellow stone. Knuckles looks somewhat amazed, but tells them that lucky they already have some. Sonic tells him where are they; Knuckles soon tells Sonic that the Dark Legion tried to offered the two stones to Eggman, but our resistance group was strong enough to thwart that attempt. Sonic then informs that he has to get them himself, but Knuckles refuses. Tails believing Sonic is on to something believes maybe he should have those stones. Knuckles tells them no matter what, outside forces cannot have what is already possessed by the echidnas. Sonic then wonders if your clan want all the stones to make a weapon, but Knuckles disagree. He tells them that if they have all the stones, they won't unite it, but honor their collective power. Sonic then mentions about the Centrum. Knuckles said our Mitre is one of the guardians of the Centrum.
Sonic tells Knuckles, that if they have one best shot to defeat Eggman, he himself must find all those stones. Knuckles pondering if this wrong, but Sonic makes a deal that if he stops Eggman with the stones. He will let Knuckles and his Echidna clan watch over them and tell Zugo that it is being safely protected. Tails senses it is a great idea and both of them will get what they want. Knuckles eventually concur. Knuckles soon guide them to the Grand Temple and get the two stones—the green and red. When they hear the Mitre coming, they all escape and as they venture off Necropolis, Knuckles tells Sonic he will join them to make sure he make due to their agreement. And soon they are on their way to the other four.
Back in Robotnik's lair, the mad doctor leaves out of a mysterious room labeled "Laboratory X". As he heads off, he is soon stop by E-100 where it informs to his maker that the hedgehog it let alive are after the stones. Robotnik gets mad and demeans his commander. However, Robotnik tells E-100 that you will lead its group of upgraded robots and go after that annoying hedgehog and stop him with whatever means. E-100 acknowledges and heads off to command its group. Robotnik then heads to a lower compartment as he observes the construction of a nearly-finished, massive spear. Robotnik then says to himself that time is near for his Death Egg to be complete. He laughs sinisterly.
Somewhere around the mountainous area, E-123 carrying Amy heads off as E-123 wonder where to go now. Amy believing not back home, so deciding to bring her to the nearest town. E-123 acknowledges and increases his jet power. Meantime, Sonic, Tails, and Knuckles soon head to Pyrite Town, a local town fill with various creatures. Sonic sense the stones somewhere, Tails soon wonder where it could be among this group. Knuckles tell them to look out for enemies; Eggman might caught wine of their mission. Being aware of who they meet, they soon meet up a interesting pair nearby the Pyrite Fishing Grounds. They soon meet Cream the Rabbit and Big the Cat along with their pet buddies Froggy and Cho. Sonic smiling after Big trying to fish his best catch of the day; Cream insists that Big is her overprotective big brother and just trying to keep us fed. Tails wonder if they are all alone; Cream tells their story about them being adopted and that their parents left and never came back.
As Cream explains her and Big's story, Sonic senses the stones. Big then shouts that he has something. And then he pulls out a blue stone out from the pond. Sonic and the others are surprised; Cream seems happy. However, Knuckles explains the reason just like he told Sonic and Tails. Sonic tries to grab the blue stone, but Big refuses to let go. Cream tells them that the blue one is their second. She rushes inside her hut and run out to show the others another stone, a cyan stone. Sonic is amazed that the fourth and fifth is right there, but need to persuade Big and Cream he needs the stones more. Sonic then tells them about Eggman; and that if Eggman ruined his home and almost ruined Knuckles, he won't blink for a second to ruin Pyrite Town. Big and Cream look at each other and realize their safety and the town's safety is much more important than what Big says stupid colored rocks. Big and Cream soon gives Sonic the blue and cyan stones and tells him to do what you need. As they head out, Sonic wonders if they want to come, but Cream tells him she and Big will remain home and at least keep an eye amongst the townsfolk.
Sonic, Tails, and Knuckles continue their way as they leave Pyrite Town and venture to the next closest place. Over next day or two, they soon venture to a visiting market town known as Orco. Once there, they stop rest and eat. During their meal, Sonic starts to reminisce his friends such as Amy and Monty; and think about Sage. He left Sage and not even letting Sage finish what he had to say back in the Great Hall. Clearly upset, he then pounds his fist to the table alerting Tails and Knuckles. Tails wonder if he is thinking about what happened to his home; Sonic not replying, but shaking his head in agreement. Knuckles with his hard knock attitude tell Sonic that Eggman creep will pay for what he has done. Sonic soon think about what Zugo said about letting his emotions get in the way and that is a distraction, and not a tool to defeat. Sonic tells Knuckles he doesn't forgive and will never forget what Eggman did, but getting all the stones at least will have hope. Tails agrees; Knuckles just wonder where the next stone would be. They already have five, where are the last two.
Before they can focus and think what to do next, Sonic soon hears a female's voice screaming out his name. Sonic soon realizes that voice came from Amy. Sonic yells out her name and runs to her. They reunite embracing a hug; and Amy out of the blue kisses Sonic on the lips. Sonic getting blush over that soon notices a bot very similar to the one that killed Monty is right behind her. Sonic tells Amy to get behind him as Tails and Knuckles come beside Sonic to shield Amy. Amy tells them E-123 doesn't mean any harm. Sonic is surprised and reminds her, what its fellow bots did to their home; did to Monty. Amy knows that, but keeps telling Sonic and the others E-123 won't harm us. Knuckles wonder how she know that. She tells them it brought her here; if it wasn't for E-123, she would've been still being held captive alongside the others. Sonic tells her where the others are. Amy tells Sonic Sage and the others are somewhere in a mountain cavern being held captive by Dr. Robotnik. Sonic and the others confused on that name until Tails mention does he look very eggish. Amy says yeah, and Tails believe Eggman and Dr. Robotnik has to be the same person. E-123 soon tells them that it can show them where to find him, Sonic tells him no. Amy is mad and wants to know why. Sonic tells her that first things first they need to find the rest of the stones; and then they will rescue Sage and the others. Amy still mad and upset, yet feels like he knows what he is doing.
Knuckles then reiterates where to go now. Sonic ponders about it until Tails mention a story his older brother told him. He said that his brother told him a folklore about a sky fortress having to watch over a stone of mystical power. Sonic believes it has to be one of the remaining stones; he tells Tails does he know where is it. Tails tells him that he doesn't know the exact location in the air, but remembered from his brother that to get to the fortress you have to come across a tower. Amy then tells them that she spotted a tower nearby from here when she and E-123 came here. Sonic and the others are ecstatic and tells her where she saw it. Amy soon shows them the way; she tells E-123 to carry her. E-123 carrying Amy flies off; Sonic uses his speed; Tails grabs Knuckles hands and fly off as well.
As Sonic and his friends head west towards the mountainous region, they are soon attacked by a squad of flying robots. Sonic then turns to see other robots marching on foot to him. Sonic tells Tails and Knuckles to do what they can with those flying bolts and nuts while he takes care of the cog heads on the ground. Sonic soon uses his speed to blast off and attack the bots while Tails and Knuckle team up in the air to take down the bots flying. As the bots are destroyed, more approach and soon E-100 arrives. Sonic sees the killer bot and wants to make sure it will pay personally for killing Monty. E-100 laughs and then fires at Sonic; Sonic dodges his attacks, but then bomber bots appear. And when Sonic steps on one, it explodes. Amy sees what is going on there and screams Sonic's name. She tells E-123 to get down there. E-123 don't know, but she reminds him if its program is to guard then guard Sonic. E-123 taking the acknowledgement and flies down to help. As Sonic gets up, E-100 steps hard on Sonic to pen him to ground; it soon aims its gun barrel facing Sonic, E-100 can only say, that he will join the other weak hedgehogs including the one it eliminated. Sonic gets angry and before Sonic can do anything, E-123 spears E-100. Amy helps Sonic.
As Sonic looks on to see E-123 fighting off E-100, Amy soon points Sonic to the spiral tower close by. Before they get there, the two E-bots continue to battle; until E-100 lays a sneak shot towards E-123's lower waist. E-123 gets hit hard and falls to the ground; E-100 then walks towards E-100 and tells E-123 is a traitor. E-123 tells E-100 that he chose to fight, and that he will not guard anymore. E-100 can only reply so be it; then E-100 fires its blasts to E-123 destroying it into pieces. Amy cries no and E-123's name; then E-123's severed head comes towards them. It is able to continue to speak and tells Sonic and Amy to go on; go to the tower. Sonic heeding the words, carries Amy and speeds off towards the tower. E-100 then crushes E-123's head and then looks at the hedgehogs running.
They soon enter the tower; Sonic carrying Amy speeds quickly around the tower stairs all the way to the top. When they reach the top, they soon see Tails and Knuckles arriving as well. Knuckles now what. Sonic then looks up and read inscription above the tower ceiling. He yells out, "We come from ground to seek the fortress' eye, take us now bring us to the sky!" Then a mystical power wind appears around them; they are soon swirl around in the wind as it disappears. E-100 and some robots soon fly to the top to see the hedgehogs and the others gone. Not known what happened to them, they fly away.
Flashes above the skies, where a sky kingdom is seen and then the mystical wind appears. Sonic, Amy, Tails, and Knuckles are out of the wind as the wind disappears. They look around to see that Tails' folklore story is true. As they venture the fortress, Sonic wonders where is the stone. Tails mention that when Sonic said that inscription, it said the fortress' eye. Sonic thinks the stone is this fortress' eye. Knuckles ponder where it could it be and Amy points to the castle fort where she sees something shining. Sonic believes it has to be the stone. Tails wonder how can they get there; the others look to each other and look at Tails. Tails realize he can fly.
Tails fly towards the fort as he observes a white stone and believes it is one of the Chaos Emeralds. He yells out to the others that its there. Knuckles then yell out and go on get it! Tails then reach inside the open tower roof to get the stone, however he gets attacked by figures. Tails screams. The others hear his cry, Sonic wondering what's up and speeds forward to reach the top. He spins in a circle and using his speed; he super jumps to the top of the fort's tower. Getting inside, Sonic sees Tails being taken away by armored guards. Sonic knocks the guards out with his speed and saves Tails. Before can they go back, a door opens to see what looks like a figure top with the crown. The figure tells them why they are here invading us. Sonic tells the figure they don't mean harm, just need the stone. The figure reveals himself as King Avalon the Falcon; and tells them no way. Sonic explains the reason if they don't and if not this evil madman known as Eggman will attack the fortress and its people. Avalon starts to think; Tails tells him the Fortress' eye will help in a big way. Avalon understands and relents. He agrees for them to take the eye, but need something to replace it. Sonic then tells them why don't look up deep in the sky, the true fortress' eye is in the stars. Avalon takes upon the idea and agree. Sonic and Tails feel proud; they soon leave but not forgetting the white stone. Avalon looks on that and hope they protect that stone well, while he soon looks up to see the deep sky and start noticing a star twinkling. He smiles hoping that is the true fortress' eye.
Grabbing the next to last stone, Sonic and the others wonder how to get back. Tails soon tells Sonic to revert the inscription in a way we want to go back. Sonic likes that and as he ponder what was the saying; he reverts it as "We gain the eye, we are here now. Take us from the sky straight to the ground." Then the mystical wind reappears, as Knuckles mentions here we go again. The wind takes them away and disappears below. Seconds later, the gang are returned back to the top of the spiral tower. The wind goes away. Amy wonders are they ever going to back to save the other hedgehogs. Sonic mention in due time. And then we see a huge airship uncloaking itself. The gang is stunned as they see the ship. Then a screen appears and on the screen is an image of Dr. Robotnik/Eggman. The others seem to be paralyzed; and then Robotnik says to them in due time in deed. He soon laughs as an army of robots surrounds the group.
Sonic and the others are soon taken to the Eggman Cavern deep inside Robotnik's underground lair. As they are march near the hangar bay, Robotnik walks nearby and informs them that resistance is futile. Sonic then tells him no matter what Eggfreak, the doc won't win. Robotnik disagrees and tells Sonic or in his terms blue menace as Robotnik presses a button inside his control room. He tells them meet the world's end. They soon see a massive metallic egg-like sphere rising from the deeper ground. The others are completely surprised. Robotnik then tells them meet the Death Egg. Sonic mentions he won't get away from this; and Robotnik mentions on contrary blue menace and then explains he needs substantial energy to fuel his weapon and then he mentions about the captive hedgehogs. Sonic and Amy are confused, but then Tails thinks what Eggman is doing. He soon is horrified and tells them that what Robotnik meant is by stealing the Hedgehogs' energy. Sonic then looks at Robotnik and tells him he's a soulless monster. Robotnik smirks sinisterly and giggles; he then states that the fox boy is right. Energy from the hedgehogs will drive the Death Egg, but he needs a engine. He then stares at the stones as E-100 taking possession of the six stones brings them to Robotnik. Sonic notices what the doc meant as he realizes the doc needs the stones to control the weapon.
Robotnik then tells his robots to bring his guests to the piranha dungeon. Sonic realizes there are seven stones, they already found six. Sonic destroys one bot and then looks to Robotnik and tells him he's missing a stone. Robotnik appears horrified, but then laughs. He then shows Sonic a compartment inside the Death Egg. Where on a seven-slot disc, there is the seventh stone—the violet stone. Robotnik then turn to his hedgehog guest and tells him thanks for making sure there were seven. He then tells Sonic and Amy soon your energies will be part of the weapon. But needs to install the other stones, so he orders his robots to bring them to the piranha dungeon. As they are taken away, Robotnik begins to install the other six stones.
As they are taken to the dungeon where below a pool are hungry robotic piranhas, Sonic looks to Knuckles. They both use their strength to battle the robots; they soon knock them down into the pool. Sonic speeds to knock the other two robots who were keeping hold of Amy and Tails down with his other robot decease friends. Amy tells them they know where the others are. Sonic tells Knuckles and Tails to go see if there is a way out of this place, while Sonic and Amy head to find the captive hedgehogs. As Knuckles and Tails head north, Sonic and Amy head south.
Minutes later, Sonic and Amy head to the place where the other hedgehogs are being kept. Sonic sees the robot guards coming this way. He soon destroys the guards as Amy tells him to go after the computers. Sonic does so destroying the computers; doing that, it causes the force field that was shielding the captives to dissipate. Sonic and Amy sees their fellow hedgehogs weaken and realize their energies were drained by Robotnik. Amy tends to the others while Sonic run to Sage, who unlike the rest appears the weakest. Sage is glad Sonic made it and knew all along it would be him to save the world. Sonic seems Sage is talking like if this is his last, and then Sage tells Sonic that he did what he can to be the current guardian and explains to Sonic the real reason why he brought him to the Great Hall was that Sonic was always meant to be the guardian. Sage said Serio will be proud, and as so as he. He then tells Sonic my time here is done. It's time to move on. Sonic starts to tear up but refuses; Sage tells him it is okay to cry. The only time Sonic cried was when his father died, and this will be the second. Before long, Sage closes his eyes and slumps in Sonic's arms. Sonic is upset; a tear begins to show and he then screams no. Amy and the others see Sage passing away, and they all are upset. Amy even shears a tear.
Then out of nowhere, E-100 and his few robots arrive. Sonic sees the bots and sees E-100. He rests Sage down slowly and quietly; Sonic rises up, shaking his fist. Sonic then looks at E-100 and tells the bot, its your time to join your weaken robots. Sonic then speeds quickly and kicks the surrounding destroying them. E-100 tries to fire, and then Sonic thinks how it attacked E-123 realizes to do the same. He then super kicks in lower section. As the power of the kick, rips E-100 into two parts. E-100 hit the floor only with its head and torso. Sonic then looks at it and tells E-100, Monty and E-123 wanted to say hello. Sonic then stomps hard on E-100's head crushing it. Amy smiles and claps congratulating that robot's defeat, but Sonic tells her it's not over. He then tells her to bring the others and find Tails and Knuckles. Amy wanted to know where is going; Sonic where mention it's time to do some unfinished business. Sonic speeds away. Amy heeding Sonic's orders tells the others to follow her.
Sonic eventually heads to the hangar where Robotnik is already aboard his airship as it carries its Death Egg inside the ship. Sonic needing to find a way there. Decide to use his speed as he jumps off a surface and jumps off another surface as the ship departs. Sonic soon jumps into the back of ths ship. He enters as he battles numerous robots. He soon heads to the dock to see Robotnik smiling and telling he has to give the blue menace credit. However, it is too late. Sonic tells Robotnik it is never too late. He speeds to head to controls until Robotnik fires a shock bot. The bot stuns Sonic; he tries to use his speed, but gets stun. He tries to get the bot off of him, but no use. Robotnik tells Sonic that the bot is specialized to hold off the speed thus eliminating one of Sonic's strengths. Robotnik smiles and laughs as he walks towards Sonic; Robotnik then opens up the bottom of the ship. Robotnik then tells Sonic that once the Death Egg will be drop, life will be eliminated. Robotic life will soon take foot. He will be the king of Planet Robotnik. Sonic turns to see the weapon and then as he continues to get weak, he begins to have flashbacks. Flashbacks of him and Monty racing; hugging Sage from an earlier time; Amy, Tails, and Knuckles. Zugo's voice is heard reminding Sonic he is the one to find the stones and the stones will call upon him.
Inside the weapon, all of the stones glow and then Sonic sensing the call of the stones. He makes a fist and rises up. Fuel with passion, Sonic rips the shock bot away from him. Robotnik looks on and yells no. Sonic then says yes; he then super speeds straight to the weapon. He then jumps and breaks into the Death Egg right in the spot the seven stones are and grabs all of them. Robotnik yells no again and fires his blaster again and again. Sonic dodges the blasts; as he then senses the power of the stones. he takes them all and closes his eyes. He focuses hard and tells himself that he is ready to accept the stones. The power of the stones soon glow higher as the glowing rainbow aura engulfs Sonic cocooning himself. Robotnik unknown of what is happening fires his blaster again at Sonic. However, the shock waves has no effect. Inside the makeshift cocoon, Sonic is transforming; his blue skin changes to gold; his eyes transforming from green to red. Then cocoon breaks as Sonic looks towards Robotnik; Robotnik completely look flabbergasted. Sonic in a transformed look appears much stronger than before. Robotnik realizing he won't waste time drops the Death Egg even without the stones in it. He tells Sonic that even if the stones not inside, it still has enough power to destroy at least an island.
Sonic notices the Death Egg falling and has sights on South Island; Sonic having confidence in his new strength jumps down to stop it. Below Tails, Knuckles, Amy, and the freed hedgehogs look up in the sky to see the weapon falling and something else. Amy wonder what is the other thing that dropped; Tails fly to get a closer look to see its Sonic, but tells them he looks different. Confusing the rest. Back in the air as the Death Egg falling down, Sonic decides to use one of his new powers. He creates a super sonic boost where he cloaks himself in a fiery aura and increases his speed where instead of stopping it; he bypasses it and reverts direction. He then uses his super sonic boost and super kicks the weapon in reverse. The Death Egg instead of falling is ascending in a increasingly rate. Robotnik looks on in horror and, "curse that blue hedgehog!" As he screams no, the Death Egg hits Robotnik's ship exploding the cockpit from within and parts of the ship. The other half of the ship falls down to the mountain that keeps the Eggman underground lair. The ruin ship crashes causing an volcano eruption-like explosion. Tails, Knuckles, Amy, and the others run to escape the remains of the mountain exploding; soon they reach to a secure place.
Sonic soon lands a bit hard and then his blue skin, and green eye appearance reappears. All seven stones reappear as well; Knuckles soon grab hold of them. Tails and Amy help Sonic get back to his feet. Everyone wonder what was that transformation. Sonic kind of nicknames his golden appearance as sort of a "Super Sonic mode." Amy wonders if he will do that again; before Sonic can say anything, Knuckles remember Sonic of the deal they made. Sonic didn't forget; soon Zugo appears. Sonic shock to see him. Zugo tells Sonic that you saved the day; found all the stones; and defeated Robotnik the right way.
Sonic wonders if Zugo wants the stones; Zugo tells him, that he maybe the guardian, but realizes the Echidnas are more suited to keep an eye on the stones. Sonic then wonder if this was ever his destiny. Zugo tells him saving your hedgehog clan, finding the stones, and accepting the stones' power; is not his destiny. Sonic wonders what is. Before anything else, Zugo can only tell him that his road is much broader than before; and that if he forgot his way, he will. And with that, Zugo flies off. Sonic seems baffled to what Zugo had to say, but understands somewhat. Amy wonders can they go back Spring Hills. Sonic says no, and that he is that he is the new guardian of his clan. They should follow him. Tails tell them they can follow him to his home, Westside Island. Sonic look to the others and tell Tails that they will talk about it. Knuckles soon tells Sonic that if he still wants the stones. Sonic thinking if he wants that awesome transformation again, he agrees, but tells Knuckles if only they can race for it. Knuckles taking this as a challenge agrees. As Sonic and Knuckles get ready, Sonic think about the unfinished race he promised Monty and somewhat sees Monty in Knuckles. As Knuckles is about to say ready, Sonic is a like mile ahead of him. Knuckles tells him no fair, but Sonic didn't hear go yet. Knuckles smirking begin to run. As he is nearby Sonic, they begin racing; while Tails, Amy, and the others look on to observe.
In a post-credits scene, deep inside the ruined Robotnik's lair, zoom into a broken door labeled the mysterious Laboratory X. Among the ruin beams and broken computers, a hibernation chamber is still active. Soon view a nameplate titled "Project Doom". Then a meter beeps green as a computer mentions "Hibernation complete." Inside the tube chamber is some type of green liquid and then a hedgehog-like figure starting to move. It soon opens up its red-black eyes. Thus kicking off a possible sequel.
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