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Bowser was in his castle watching footage of his constant defeats at the hands of Mario, but since he could not find the plumber's weak spot, so he sent his minions to every corner of the Mushroom Universe to gather information, like Shooting Star Summit, Beanbean Kingdom, Vibe Island, Melody Bay, etc. He divide his army into 14 groups, one commanded by Goomboss, the second one by King Boo, the third one by Kammy Koopa, the fourth one by Kamek, he left the other eight groups in the hands of each Koopaling and the last one guards Bowser's castle. But each group discovers evidence that a long time ago, there existed an Ancient and powerful Koopa Troop trapped in another dimension! Then, thinking he can beat Mario once and for all, Bowser commands the opening of the portal. But then, the Ancient Koopa Troop went around the Mushroom Universe destroying everything in their sight, including Bowser's Castle . Bowser roars at his minions blaming them for what happened for a while, and then, after he calms down, he decides to chase down the Ancient Koopa Troop. Meanwhile, Kamek stayed behind and looked up these notable members of the ancient troop:
They included The Para Trio : Heatroopa, Electroopa and Artictroopa, -The Chomp Trio : Spyro Chomp, Ray Chomp and Water Chomp -The Mineral Series: Koorock, Kooice, Koosteel and their leader Koogigas -The Weather Controlling Members: Terrakoopa, Tidal Koopa and Sky Koopa -The Mystic Beasts: Silvertroopa, Goldtroopa and Rainbowtroopa -The Ultimate Ghost, Fearkoopa -The Volcano Inhabitants, Firebeetles -The Dream Master, Nightmare Koopa and the leaders of the troop, the most terrible members of all, Koodialga, Koopalkia and Bowseus.
Kamek suggested for Bowser to travel through the Spin Dig Galaxy, so he did, defeating ancient Koopa Troop soldiers, until suddenly, he heard a faint cry for help. He questioned this and traveled through the galaxy until he saw the Para Trio holding his Rocky Wrench Squad captive. Heatroopa, Electroopa and Arctictroopa let Bowser in on their plan. Enraged that his troops were being held captive, Bowser engaged the trio in battle and with Kamek's help over Bowser's video watch, Bowser sent the three to their leaders. Bowser frees the Rocky Wrenches and they teach Bowser a new special attack. Thinking that the other troops were still out there, Kamek notifys Bowser that he sent out more troops, like Big Bob-omb, Petey Piranha, Broggy, Army Hammer Bro. and around 8 more, since there was no sign of the other troops. Bowser then knew he had to hurry, so he moved on to Bob-omb Battlefield to defeat more ancient Koopas...
Meanwhile, in another dimension, Heatroopa, Arctictroopa and Electroopa, tell Koodialga, Koopalkia and Bowseus about Bowser's victory and the freedom of the Rocky Wrenches. Because of their loss, Bowseus destroys the 3 Koopas and sends Spyro Chomp, Ray Chomp and Water Chomp to handle Bowser in Bob-omb Battlefield. The Chomps are transported as Koodialga, Koopalkia and Bowseus laugh manaiaclly, ending the cutscene...
Bowser has to go through this area in a similar fashion to Super Mario 64, having to go through levels which involve finding the red coins, beating Koopa the Quick and of course, freeing Big Bob-omb and the rest of the Bob-ombs and learning another special attack. After Bowser is done with every mission, he has to talk to a special Bob-omb Buddy who tells him that if he's lighted, he can take Bowser to the final mission in the sky. Bowser then accepts and he is launched into an arena.
Bowser then hears three voices and sees the Chomp Trio! He is informed of more of the big plan to take over the Mushroom Kingdom and informs Bowser that Bowseus is holding Bowser Jr. captive. Enraged by this news, Bowser engages in battle and after a long battle, completely annihalates the trio! Bowser roars in triumph and jumps off of the arena only to meet Mario who he instantly engages in battle, but because of the condition that the Chomp Trio put Bowser in, he loses almost instantly. But, thinking that Mario can help him from inside, Bowser is forced to ask Mario to help him defeat the Ancient Koopa Troop. Mario agrees and he gets sucked in again. Bowser is recommended to head toward Isle Delfino to find the Piranha Plant Patrol. Bowser first returns to his castle and gets his swim trunks and beach gear and then leaves.
Bowseus is enraged at Bowser's constant victories, so he sends an army of over 5,000 Firebeetles to slay Bowser and warns them that if they fail, their race will be completely wiped out. The Firebeetles moves as fast as possible to Isle Delfino. Once again, Bowseus' manaiacal laughter ends the scene...
On the way to Isle Delfino, Bowser's plane is hijacked by a gang of Flying Firebeetles. Bowser decides to battle them for control of the plane. After they are tossed off of the plane, Bowser steers straight to the Delfino Airstrip. When he swims to Ricco Harbor, a gang of Piantas try to throw the tyrant in Delfino Prison. Mario jumps out of Bowser's body and explains to the Piantas that it is for a good cause that Bowser is here. Knowing that, the Piantas cautiously release Bowser.
An extra cutscene occurs in which Kamek's video watch picks up the location of the other patrols. But, when he is about to report to Bowser, Koorock and Kooice, spot Kamek and cage the poor Magikoopa!! Luckily, Kamek managed to send the message to Bowser with a call for help and the patrols' coordinates.
A little later, after the Piranha Plant Patrol is found, Kamek's message comes through and Bowser hurries to the airstrip. Soon enough, he is halted by Lord Firebeetle who engages Bowser in battle. The battle proceeds, but when Bowser is about to deal the final blow, Lord Firebeetle yells to cease the battle. A cutscene then occurs, in which Lord Firebeetle tells about his situation. Bowser intently listens, yet in the end, he kills Lord Firebeetle and moves on to the airstrip.
In flight, Bowser mulls over what has happened and decides to head to Peach's Castle, where the Goomba Gang is being held by the Mineral Series. He is halted by Toads, similar to on Isle Delfino and once again, Mario explains their cause and the Toads give the duo an escort to be safe. Bowser goes through until he finds Goomboss and his squad stuck in a cage. He tries to melt them out and punch and do all that he can, but he is halted by the Mineral Series. Koogigas tells Bowser that he needs the key made of the trio's dead bodies. Bowser then enters a duel to the death and when he wins, Koogigas runs away and Bowser frees his Goombas. They all cheer and crowd their king and soon, they all leave the castle.
Meanwhile in the Negative Universe, Bowseus is so angry that his castle is falling apart due to his rage. He sends out one of the Mystic Beasts, Silvertroopa. Since this ancient deity has never failed, Bowseus has great confidence in his certain win...