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Rouge down in the hanger she begins to transmit data as the colony begins to shake. Shadow and Sonic continue their battle as Sonic spots a power ring he uses it to knock Shadow down. As the colony continues to shake, Shadow speeds off and Sonic spots a counter. Eggman and the others are in the control room as the chaos emeralds are taken away. The watch the message as Gerald continues his message saying he'll destroy everything because of Maria's death so they can feel his pain. Eggman explains who he was to Amy and the others as the colony continues to descend. Rouge appears and says the colony is locked into its decent. Eggman says destroying the planet is one thing, but destroying him is another.

Just then Sonic appears and wonders what is going on, Eggman says he won't give him a showdown. Sonic says if they work together they may be able to get things done. Eggman shows them the journal entry about the project and he used his time to plan his revenge and that Shadow will bring total destruction to the planet. The president is informed the colony is moving at high speed towards the planet and Sam wishes him luck. The police meanwhile arrest the secret group that were holding the files.

At the colony Eggman informs that the explosion will cause a super nova and Tails says the emeralds have to be deactivated. Knuckles figures out he can use the Master Emerald to shut the chaos emeralds down. They decide to work together to take down the emeralds. Tails, Eggman, and Rouge work to open the security doors as various traps go off trying to stop them. With Knuckles and Sonic in lead Decoe and Becoe work to carry the emerald behind them. Tanaka, Chris, and Amy stand by watching. Just then Shadow appears and says that they won't be able to make it.

As ARK continues to fall to the ground Chris pleads with Shadow to save everyone instead of believing that he is there for revenge. He reminds Shadow that he was created to save others, Shadow attacks Chris, but he gets up telling Shadow that getting revenge won't bring Maria back. Chris continues to pled saying that people alive today cannot be blamed for deeds done in the past, it isn't fair. Shadows tells him not to tell him what is fair, Shadow says that he tried to save her but there were too many people for him to save her. Chris says that it is true that there are some bad people in the world, but most are good, he continues to beg Shadow telling him that Maria would want him to be friends with people. He remembers a promise that Maria says she wanted him to be friends with people and that she hopes he'll be happy down there. Maria says that he was created to help the people on Earth cope with their problems. As Chris passes out Shadow catches him and stares blankly. Tanaka comes and gets Chris and Shadow says Chris was right and with that he smiles.

With less than ten minutes left Sonic and the others find the inner chamber where there is a shrine of the emeralds. Just then the bio-lizard appears and as they go to fight Shadow appears and tells them that he will handle the monster. Sonic and Knuckles head off as Shadow starts his battle with the monster. Shadow attacks the beast in its weak spot as Knuckles starts to chant the saying he uses the Master Emerald to stop the chaos emeralds. Shadow takes out the bio-lizard as the Master Emerald deactivates the chaos emeralds.

However the bio-lizard disappears into the light using chaos control as it ha merged with the colony pulling people towards the planet. Sonic and Shadow then decide to work together and use the emeralds to turn into Super Sonic and Super Shadow. They speed through with Sonic appearing in the same room as Chris before taking off again. The two appear outside the colony and fight the biohazard.

The colony continues to descend into the atmosphere as everyone stares up into the sky watching the battle continue up there. Super Sonic and Super Shadow continue their battle. Scarlet goes on TV and tells people what all has happened and that Sonic and Shadow fight to keep them safe. As Sonic and Shadow continue their assault they destroy the beast and use their combined powers to try and stop the colony. Unleashing their full power the rings around Shadow's wrist explode off and he they both use their full strength to use chaos control on the colony.

In a blast of light the colony reappears in safe orbit with the people of Earth celebrating. As the aid says Sonic can still be brought to trial, Sam explains the voters would not be happy if they did that. Eggman talks to the others saying that he wanted to be like his grandfather saying that his grandfather was wrong for trying to destroy the planet. Eggman than says he will still try to take over the planet as Sonic reappears in the room. Chris steps forward to learn that Shadow has disappeared and he hands one of the power rings to Chris. Rouge says that Shadow may have been there to stop his crazy plan. Sonic says Shadow sacrificed everything to save them all as Sonic has them head back to the planet. And with that they leave the colony as it begins to go into hibernation Sonic bids farewell to Shadow and walks away.