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Sonic, Knuckles, and Tails reunite against a powerful new adversary, Shadow, a mysterious villain with powers unlike anything they have faced before. With their abilities outmatched, Team Sonic must seek out an unlikely alliance.

Sonic, Knuckles, and Tails reunite against a powerful new adversary, Shadow, a mysterious villain with powers unlike anything they have faced before. With their abilities outmatched in every way, Team Sonic must seek out an unlikely alliance in hopes of stopping Shadow and protecting the planet.

A top secret weapon, Project Shadow reawakens and cause destruction across the world. Team Sonic try to intervene but Shadow's powers are too much for the crew to handle. Sonic then decides to team up with Robotnik as they go on a global adventure to stop Shadow.

After being imprisoned for 50 years, the mysterious hedgehog Shadow escapes captivity and starts wreaking havoc all over the world. Now Sonic, along with Tails and Knuckles work with Team GUN to try and take him down. But when Shadow proves to be too powerful, Sonic and company have no choice but to team up with their old nemesis Dr. Robotnik in a difficult alliance. Now it's a race against time as Sonic must uncover the secret of Shadow and fight an enemy too powerful to defeat alone.—Blazer346

In Tokyo, a prison for the corporation G.U.N.s security is breached, waking up Shadow and allowing him to make his escape. Meanwhile, Sonic is celebrating his anniversary since arriving on Earth with Tails and Knuckles, when the G.U.N. Director, Rockwell arrives and announces Shadows escape. Rockwell recruits the trio and calls them "Team Sonic".

The trio battle Shadow, only to discover that he is way stronger than them and he runs away. Team Sonic go to meet G.U.N. commander Walters and he reveals that the corporation had discovered Shadow in 1974 in a meteorite. Shadow used his powers for various experiments, but things took a turn for the worse, the project leader was arrested and Shadow was put into stasis. To make matters worse, Dr Robotnik arrives with an army of drones, fatally wounding Walters. Just before he dies, Walters hands Sonic a digital key card and asks him to remain safe. Team Sonic don't know who to trust anymore, so they decide to battle Shadow without the aid of G.U.N. Agent Stone reveals that Robotnik is still living and didn't send the drones. The trio join Robotnik and they follow the drones to a deserted G.U.N. base.

Shadow reminisces about the project leader's granddaughter Maria and how he used to hang out with her as his one true friend. One fateful night, as they attempted to escape the base, one agent set off an explosion, killing Maria. Shadow becomes devastated and vows revenge on all humanity. He captures Team Sonic and Robotnik meets his long lost grandfather Gerald. Gerald was imprisoned for the last 50 years.

Gerald tells them that there are in fact, two key cards required to activate the Eclipse Cannon, an orbital laser that has the potential to destroy any location on Earth. Gerald plots to use it to destroy G.U.N.s headquarters and Ivo joins him, stabbing Sonic in the back. Shadow snatches the key card from Sonic and tries to destroy them, but Team Sonic escape safe.

Team Sonic travel through a ring portal, before recruiting Tom and Maddie to help them. They travel to London, but Shadow fatally injuries Tom in the process. Shadow robs the second key card. Ivo, Gerald and Shadow launch the Eclipse Cannon, but Sonic is so mad about him hurting Tom that he abandons Tails and Knuckles and steals the Master Emerald, ultimately transforming him into super Sonic.

Sonic rushes to the Eclipse Cannon, now located in outer space and confronts Shadow. Shadow and Sonic once again fight each other and Shadow absorbs some of the Emerald energy. Sonic finally overpowers Shadow, only to come to the realization that he has given in to vengeance. Sonic tells Shadow about the loss of Longclaw years prior, announcing that the people they have lost are way more important than vengeance. Shadow finds Sonics speech beautiful and apologizes for his actions. The duo agree to stop the Eclipse Cannon.

Gerald announces to Ivo that he plans to use the cannon to destroy the entire planet for revenge of Maria's death. Ivo wants to conquer the world as opposed to destroying it and the two engage in battle. Tails and Knuckles help Ivo to push Gerald into an energy field, ultimately vaporizing him. Together, the team are able to deflect the cannon away from Earth and it destroys the moon instead. Just as the cannons core begins a melt down, Robotnik and Shadow sacrifice themselves and move the cannon out of range of planet Earth. The cannon eventually explodes.

Back on Earth, Sonic reconciles with Tails, Knuckles and Tom, and Tom recovers from his injury. As the credits roll, Sonic comes across multiple versions of himself, which are robots only to be saved by a female pink hedgehog. Shadow is also revealed to have survived the explosion.