Meanwhile Sonic and Shadow are still fighting when Sonic sees a ring. He grabs it and uses it to defeat Shadow. He then asks him what is going on, to which Shadow replies, "You'll find out." The ARK starts shaking again, and Shadow tells Sonic his time is running out and runs away. Sonic then sees the timer counting down.
Chris Thorndyke, Tanaka, Amy, Tails, and Knuckles, with the Master Emerald, enter the room Dr. Eggman is in to hear him say he got tricked by his own grandfather. A hatch then closes with the Chaos Emeralds keeping them away from everyone else.
A screen then plays with Professor Gerald Robotnik saying that his final revenge had begun, and that Space Colony ARK would plummet down to the planet with devastating force and destroy everything and everyone. He also mentions that everyone would know how he felt when he lost Maria. Amy asks who he is and what he means. Eggman then tells everyone that this man was Eggman's grandfather.
The ARK starts shaking again, and Knuckles states that it feels like it's falling apart. Rouge comes in saying it will get worse. The ARK's propulsion system computers were locked so they can't reverse course. Sonic comes in a few seconds after asking what's happening. Chris is happy to see him. Eggman tells Sonic that they will soon be destroyed, but Sonic suggests that they work together to get out of the mess.
Eggman then shows them his grandfather's diary. Chris reads the following entry revealing that the professor went insane after his granddaughter Maria was killed. When the Space Colony ARK was shut down, Maria was killed in the process. Gerald went mad because he loved Maria so much. He wanted to curse all humans, so he made the Eclipse Cannon, and when having enough power (the 7 Chaos Emeralds) would be programmed to make ARK fall to New Earth. It is revealed that Gerald made Shadow for good, to benefit man-kind but Space Colony ARK was destroyed, and as a result, so was project Ultimate Life Form A.K.A. Shadow. He was able to complete his research and finish Shadow, and he says that you may awaken it "if you wish to fill the world with destruction".
Down on the planet, the President's aide says that Space Colony ARK is definitely hurtling down to the planet and is worried in their last minutes of their lives. Sam Speed wishes Sonic luck stating that even he would have trouble saving everyone again.
Meanwhile, the people who kept Project: Shadow a secret are arrested by the police. Eggman says that the energy from the Chaos Emeralds have transformed the Eclipse Cannon into a mega-bomb. When it detonates, the blast would be more destructive than a super nova. Tails adds that the energy from the Emeralds is also what's pushing the ARK towards the planet. Sonic then looks at Knuckles. Knuckles wonders why, then Rouge reminds him that he can control the Chaos Emeralds with the Master Emerald. Soon everyone is off to get to the Emeralds. Rouge and Eggman take out laser shooters while Tails opens a passage way for Sonic, Knuckles, Decoe, and Bocoe to pass through with the Master Emerald.
Meanwhile Chris, Amy, and Tanaka wait and hope for everything to work out. Chris wonders if there's something they can do to help. Tanaka assures that Sonic will get the Emeralds stopped. A voice tells them not to bet on it. They turn and see Shadow with a smirk on his face.
Chris realizes there's something he can do to help Sonic... convince Shadow to help him. Chris asks him, but Shadow refuses and injures him. Téa then states that he made a promise to Maria, and that she was his only friend. She flashes him a peace sign, and Shadow realizes the same sign that Maria flashed him. Chris tells him that most people on the planet are good, and that Maria would want Shadow to be friends with them. Shadow then remembers the full promise he made to Maria; he would help people and be friends with them. Chris faints, but Shadow catches his fall and tears up realizing his mistake. He then goes to help Sonic.
With only 10 minutes left to go, Sonic, Knuckles, Decoe, and Bocoe make it to the Chaos Emeralds but are under attack by the Biolizard. They realize that this is the prototype of the Ultimate Life Form, Shadow being the finished product. Shadow appears and tells Sonic that he'll deal with the monster, while Sonic and Knuckles get the Emeralds. Shadow then goes off to fight the monster, and Sonic, Knuckles, Decoe, and Bocoe head for the Emeralds. With the Master Emerald in place, Knuckles recites the chant he learned from Tikal and deactivates the Chaos Emeralds.
Shadow meanwhile defeats the Biolizard, but it Chaos Controls to the outside of the ARK. Eggman's voice sounds on a communicator telling Sonic that the monster fused itself with the front of the ARK and is pulling it towards the planet.
With only a few minutes to go, before the ARK crashes, Sonic and Shadow use the Chaos Emeralds to turn into Super Sonic and Super Shadow. Super Sonic appears before Amy, Tanaka, and Chris. Sonic heals Chris with his super powers, and warps out to the front of the ARK.
He and Super Shadow then start to fight the Biolizard, which is now the Finalhazard. The President, his aid, and Sam see the red glow in the sky and the two super-powered hedgehogs fighting to stop it. Everyone hopes that Sonic can save the planet again. Sonic and Shadow defeat the Finalhazard, but the ARK is starting to enter the atmosphere. Sonic and Shadow places their hands in front of them in hopes to slow it down.
Everyone tells them that they can do it. Shadow then remembers the last part of his promise to Maria. With that, he removes his inhibitor rings to break out all the power he needs. Téa's Chaos Emerald Ring breaks, and she runs outside to look out the window just to see Sonic and Shadow. He and Sonic use a super-powered Chaos Control to put the ARK back to a stable orbit. In the end the results of Shadow using all his power caused him to lose all energy and fall to New Earth, much to both Wolf and Fox's shock.
Once back at the Great Fox, Sonic, Fox and the team come back satisfied with victory. As Sonic gives Rouge one of Shadow's rings, Chris asks him where Shadow is. Sonic gives him another of Shadow's rings as an answer. Rouge thinks that maybe Gerald wanted Shadow to stop his revenge the whole time. Sonic replies that they'll never know, but Shadow sacrificed everything to save them. Chris holds the ring close to his chest and a tear falls on it. Hearing news of Shadow's death over the video screen on the ARK, Yugi and his friends become sad, most notably Téa, who begins crying. She runs out of the room and slams her fist on the window that displays Earth, orbiting high above New Earth, in grief. When Yami Yugi appears behind her, she smacks his shoulders with her hands, asking why Shadow would do that. Yugi does his best to try and console her.
Eggman leaves with the Star Wolf Team, Orbot, Cubot, Decoe and Bocoe on the Great Fox II, stating that he still wants to take over the planet. Wolf reminds Fox that the Star Wolf will take him down one day. Sonic says that they should all head back home, and that he prefers to have his feet on solid ground. Before he exits the room, he turns and says, "Sayonara, Shadow the Hedgehog."
Similarities with gameEdit
- Galvatron is heavily shocked by Starscream's death, while Wolf is heavily shocked by Shadow's death.
- Alexis is the one who was more upset by Starscream's death, while Téa is the one who was more upset by Shadow's death.
- Rad is the one that tries to comfort Alexis, while Yugi is the one that tries to comfort Téa.
- Misty's reaction to Ash's "death" and Pikachu's failed attempts to revive him with electricity is an incredibly silent, saddened whisper of: "Please no..." while Serenity's reaction to Shadow's death and Téa's Chaos Emerald Ring broken is an incredibly silent, saddened whisper of: "No, please no."
- Carlos was present when Alexis' necklace broke upon Starscream's death, while Joey was present when Téa's Chaos Emerald Ring broke upon Shadow's overwhelming powers.
- Starscream died soon after, which sent Fred into a spiral of depression, while Shadow died soon after, which sent Tristan into a spiral of depression.
- Nick Dean screams like a girl when he encounters Poultra, while Duke Devlin screams like a girl when he encounters the Biolizard.
- Amy Rose and Chris are the ones that convince Shadow to help them.
- Orbot and Cubot only appear in the game. Therefore, they never been appeared in Sonic X before.
- Decoe and Bocoe only appear in Sonic X. Therefore, they never appeared in the game.
- Chris, Tanaka and Topaz also do not appear in the game, excluding Yugi, Téa, Joey, Tristan, Duke, Serenity and Kaiba.
- (English version only) When Sonic and Shadow use Chaos Control on the Space Colony ARK and before Shadow dies, Live and Learn from Sonic Adventure 2 plays.