After crash-landing on the Egg Carrier, Sonic, Tails, and Knuckles start to carry out their missions. Doctor Eggman immediately activates the transformed state that deactivates the monorails. Thus, Sonic and Tails go through the Sky Deck. Eggman starts launching missiles at Sonic, but he easily dodges them. One missile hits the Egg Carrier which opens up a hole. Knuckles leaves Sonic and Tails to search for the last pieces of the Master Emerald. Eggman then calls Gamma and orders him to come to the control deck. Amy makes her way out and comes to a room and plays through a game where she gets the Warrior's Feather. While venturing through Hot Shelter, she has another run-in with ZERO. When she grabs a hold of the balloon, she drifts back in time and meets Tikal after finding Chaos' Shrine. She then drifts back into the Egg Carrier. She makes it to the deck but she's caught by Bocoe and Decoe. She then pulls out her hammer but is stopped by Eggman. Sonic then says to let her go, but Amy frees herself, hits Eggman, Bocoe, and Decoe, and slams the wall making Sonic and Tails fall on Eggman. Decoe then snatches Lily, and Eggman gets Sonic and Tails off of him. He then grabs Lily's necklace and a Chaos Emerald (Cyan) pops out. He then orders Decoe to give back Lily. Gamma then comes up, and Eggman orders him to get rid of Sonic. Amy tries to get them to stop, but it does no good. Sonic defeats Gamma and is about to finish him off when Amy gets in his way. She tells him that Gamma set her and Lily free. Sonic believes her. An explosion then goes off behind them. Tails says that the ship is losing altitude. Sonic tells Tails to get Amy and Lily down to safety while he searches for Eggman. Amy manages to get Gamma to reboot. Gamma asks Amy why he saved her. She replies that she was just returning the favor he did for her earlier. The three of them then leave the Egg Carrier.
Big boards the Egg Carrier, and tries to pick up Froggy's scent, but fails, so Chris decides to find him in the Hot Shelter. He realizes that to get Froggy out. He must activate the switch. When they're about to get him, an explosion causes the floor in front of them to break. On the ground, Chuck sees Amy and Tails and takes them in his car back to the house. Tails is still worried about Sonic. Knuckles manages to find the last piece of the Master Emerald, and starts to find a way out, when he's sent back into the past again. He spots an injured Tikal and some dead Chao on the ground in front of the shrine. She tells him that she tried to stop her father, but he didn't listen to her. Knuckles is then sent back into the present and wonders why he's being sent back to the past. Big is panicking that he and Chris might not get Froggy back to safety, but a quick drink manages to calm his nerves. Big uses his fishing pole to get Froggy. After doing this and fishing Froggy out for the last time, Big turns to exit, but is transported to the past. He encounters Tikal for the first time and returns to his normal time. Big gets out of the Attendance room and heads out. When he reach the deck, he spots Chaos and Eggman.
Eggman tells Chaos that Froggy has a most unusual tail. He starts chasing Chris and Big, jumps in front of them, and knocks Big down. Big freezes in horror at the sight of him. Eggman gives Chaos 4 the Chaos Emerald (Yellow) from Froggy and the Emerald (Cyan) from Lily, turning him into Chaos 6. Froggy then hops into Chaos's body to give him back his tail. Ash tries to save him, but faceplants into Chaos 6 instead. Chris then climbs on top of Ash and attempts to rescue Froggy, but Chaos sucks them in. Froggy's tail then disappears and reappears on Chaos. Sonic then appears and sees Chris inside Chaos. He attempts to rescue him, but gets pinned down. Big carefully fishes Froggy out of Chaos's body and escapes under Sonic's orders. Knuckles shows up holding up the tentacle that had Sonic down. They both then come up with a plan to free Chris and Ash. They find Chaos' weak spot and use the Shovel Claw to get to it. Chaos 6 regenerates and attacks Sonic and Knuckles. Meowth orders Jessie and James to fire their freeze blasters, but Sonic easily dodges freeze missiles, which hits Chaos 6, freezing the beast. Sonic and Knuckles shatter a ice block containing Chaos 6, which is then reverted back to Chaos 0, and Knuckles picks up the Chaos Emeralds, saying "Yeah, you're finished!!" Sonic goes after Eggman, while Chris, Knuckles, and Big are left with the X Tornado. Team Rocket, Bocoe and Decoe have no choice but to bail out.
Back at Chris' house, Lily shows Amy a picture of her brother and sister, and that she misses them. Amy offers to help find them. Meanwhile, Sonic falls off his ride with Eggman and lands headfirst in the dirt. After getting out, he finds himself in Mystic Ruin. Meanwhile, Eggman launches a missile as a last ditch attempt (Serenity thinks it turns out to be a dud) and it lands in the middle of Station Square to set to go off in two minutes. Tails thought that Sonic would know what to do if he were here. Tails, realizing that the fate of the city is in his hands, must reach the missile first before it detonates. Angered, Eggman blasts the doors of a skyscraper and gives chase. The people nearby begin looking at Tails hoping he could defuse the missile. Tails is hesitant at first but decides to give it a go. He starts thinking of the time he first met Sonic, and how he was always there for Tails, but thinks he should start doing things on his own. He then figures out which wire to cut and successfully defuses the missile. Frustrated at his failure, Eggman unleashes an Egg Mobile - the Egg Walker, and prepares to annihilate Station Square. All of the citizens run for shelter, leaving Tails - without Sonic's help, to fight with Eggman. In the end, Tails wins and the citizens cheer.
Meanwhile, Chris, Big, and Knuckles land the X Tornado near Mystic Ruin. Knuckles goes to fully restore the Master Emerald. Big and Froggy then decide to head home. Big and Froggy are now home and enjoying peace again. Froggy is no longer insane, and Big is celebrating.
Back at the Island, Knuckles restores the Master Emerald to its normal state, allowing the giant gem to hoist Angel Island to the heavens. Knuckles is once again at peace. The Master Emerald is repaired for the first time.