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A cutscence appears showing Eggman making a plan as usual, baking a pie, listing the names of the ingredients as he adds them to the concoction. Once his pie base is created and the filling inside, he holds a bottle with a unreadable label on; "See how they like this secret ingredient!" He chuckes as he pours the contents into the already placed filling. The cutscene fades out into a zoom in on Konata, Tomo, Haruhi (your 3 playable characters for the first level) sunbathing at the beach, you automatically start Playing the level (Level 1: The Beach, Players: Konata, Tomo, Haruhi) . A bottle is washed up on the shore of the beach, your character must collect the bottle which contains a message inside, once you have collected the bottle you will see the message which reads:
There's another problem that We are Having. Dr. Eggman supposed to sign a peace treaty with you shortly after the adventure we had. But his robots have gone rogue and Eggman uses The Apple Pies to do it. We pray you avoid them until Someone have time to reprogram them. In the meantime We insist you Find Eggman and see what he's up to.
A cutscene shows Tails approching the trio, wondering what's up. They show him the letter and he warns them not to trust Eggman, but sees no harm in consuming his pie, as really what harm could come from eating a little bit of pastry? And then They deciced to fight Him, kinda not agree of what he's saying. (Level 2: Beach Enemies: Tails, Players: Konata, Tomo, Haruhi). After the Fight, They agree, and deciced to find the other heroes to help them! Tails joins Konata's Main Group (Group A).
This New Episode begins as CD-i Mario, And CD-i Luigi walking to the Mushroom Kingdom to have a pinic, and the box of Apple Pies. And Suddenly, They runs into I.M. Meen. He said that If they don't give the box to him, he'll trap in the magic book forever. They disagree and dodges Meen's Magic Spells, that aims into the Box of Apple Pies. (Level 3: The Mushroom Kingdom Enemies: I.M. Meen Players: CD-i Mario, CD-i Luigi), After Defeating him, He ran off and The Plumbers runs to the House!
Meanwhile, Konata, Tomo, Haruhi, and Tails Travels to The Fields that was fill of Baddniks and Evil Soldiers (Level 4: The Battle Field, Players: Konata, Tomo, Haruhi, Tails). Afterwards, They Spotted Dr. Eggman, they tried to chases him, but they can't because He's riding on his jet Car, and The Strange Creepy Puppets of Miyuki and Mikuru (Levels 5: The Battle Field, Enemies: Puppet Miyuki and Puppet Mikuru Players: Konata, Tomo, Haruhi, Tails) After that fight, Miyuki and Mikuru came back to their sences. The Team tells them what happening.
CD-i Mario and CD-i Luigi fighting Goombas And Koopas, and then Suddenly, Eggman dropped Evil Apple Pie Robots to fight them, and then Mario, Link, Luigi joins CD-i Mario's Main Group (Group B)! (Level 6: The Ruined House, Players: Mario, Cd-i Mario, Cd-i Luigi, Luigi, Link)
The Groups reunited, but then Eggman Catched Konata, Miyuki, Tomo and Koyomi and flyed to Australia!
The Main Group (CD-i mario, Tails, CD-i Luigi, Luigi, Link, Mikuru, Haruhi)travels to Australia and the ran into Dr. Rabbit and Kami and Shiro and Sonic as they fighting the remaining Baddniks (Level 7: The Australian Lake, Players: Cd-i Mario, Tails, CD-i Luigi, Luigi, Link, Mikuru, Haruhi, Dr. Rabbit, Kami, Shiro, Sonic)
After the battle, They Rescused Konata and Tomo, and They went inside of Eggman's Base. (Level 8: Eggman's Secret Base, Players: Cd-i Mario, Tails, CD-i Luigi, Luigi, Link, Mikuru, Haruhi, Dr. Rabbit, Kami, Shiro, Sonic, Konata, Tomo) Meanwhiles, Koyomi have somehow found the hidden key and released her prison, and tried to find Miyuki. (Level 9: Eggman Secret Base's Prison, Players: Koyomi) After Koyomi found Miyuki's cell, It's turns out that Eggman also captured Pinkie Pie, Osaka, Sakaki, Toad, Fluttershy, and Tsukasa & Kagami! They tried to escaped together and find the Main Group! (Level 9: Eggman's Secret Base's Prison, Players: Koyomi, Pinkie Pie, Osaka, Sakaki, Toad, Fluttershy, Tsukasa & Kagami) After they found the Main group that apprives at Eggman's Door. They Found Eggman, and they also found Bowser! They have to fight their Apple Pie Monster! (Level 10: EggMan's Lair, Boss: Eggman's Apple Pie Monster, Players : Cd-i Mario, Tails, CD-i Luigi, Luigi, Link, Mikuru, Haruhi, Dr. Rabbit, Kami, Shiro, Sonic, Konata, Tomo, 'Koyomi, Pinkie Pie, Osaka, Sakaki, Toad, Fluttershy, Tsukasa & Kagami) After Eggman's Defeat, Dr. Eggman decides that he cannot win in World domination with Apple pies, and gives up, and The Main Group having a party at peace, for now.
After the events of The first 3 chapters of The Egg's Apple Pie, Dr. Eggman was held in an australian jail after giving up and surrendering himself to the main hero group and the polices. He had become sick of conditions in the jail and decided to break out and redo his apple pies takeover plans, starting with the sabotage of the jail he is kept in and eventually ending at possibly full world domination. (Level 11: Australian Jail, Players: Dr. Eggman) After He finally reaches the gates he is stopped by Haruhi and Mikuru and battles them in a duel at the gates. (Level 12: The Jail Gate, Enemies: Haruhi, Mikuru Players: Dr. Eggman) Haruhi and Mikuru is defeated and Eggman grabs the gate keys, eventually escaping from the prison. Meanwhile, Spider-Man wandering around Hyrule (Level 13: Hyrule Field, Players: Spider Man) and then finds that Pit and CD-i Link fighting each other and then Spidey break out the fight, and ask them to explain what going on. Meanwhile, Dr. Eggman seeks a source of money to fund his world domination, and finds that The King, Tomo, AppleJack, Pinkie Pie is holding a talent show at dusk. Dr. Eggman finds the area after bypassing several Ponies and Soldiers and provokes The Group during part of the show thus leading to them fighting Dr. Eggman. (Level 14: The Talent Show, Enemies: Dr. Eggman, Players: The King, Tomo, AppleJack, Pinkie Pie, Chiyo, Kami) When they defeated Eggman, Eggman quickly reacts and punch Kami so hard that he tossed down into the water, nearly drowned, and rescuced by Tomo, and Trying to stop Eggman again!
The Beach: Sonic Heroes Seaside Hill
Vs. Tails: Sonic Heroes Vs Team Battle
The Mushroom Kingdom: Super Mario World Koopaling Battle
The BattleField: Super Smash Bros Brawl Gritzy Desert
Vs Puppet of Miyuki and Mikuru: SSBB music VS. Ridley (Metroid)
The Ruined House: Sonic 3 Death Egg Zone Act 1
Australia Field: Sonic 3 Death Egg Zone Act 2
Eggman's Secret Base: Sonic 3 Death Egg Zone Act 2
Eggman's Secret Base's Prison: Sonic 2 Aquatic Ruin Zone
Vs Eggman's Apple Pie Monster: Super Smash Bros Brawl Boss Theme (Subspace)
Australian jail: Kirby Super Star Ultra King Dedede
Australian Jail Gate: Kirby Squak Squad Squak Boss Theme
Hyrule Field: SSBB Legend of Zelda Main Theme
The Talent Show: Super Mario World Koopaling Battle