Rouge the Bat, elusive jewel thief, is finally caught by Lieutenant Topaz of GUN. Rouge is brought to interrogation where she’s met with Commander Tower. Tower gives Rouge a choice - spend a life sentence in prison, or become GUN’s double-agent inside Eggman’s operations. Rouge agrees to Tower’s terms, and leaves with a Chaos Emerald in hand in search of Eggman.
Dr. Eggman decides to use Protegge’s access codes to search the database of his dead brother, Teddy Robotnik, in order to find something that could defeat Sonic once and for all. Eggman finds a file titled Project: Shadow which Teddy had been looking into. Eggman investigates, and determines that Project: Shadow - the Ultimate Weapon - is exactly what he needs to take down his enemy. Eggman reactivates Metal Sonic, and tries to convince Protegge not to come on the delicate mission. Protegge really wants to come, so Eggman agrees - under the condition that she also brings her two newest creations, Orbot and Cubot, to keep her safe.
Later that day, Eggman breaks into the secure facility Prison Island, and shoots his way into the storage bay where Project: Shadow is kept. Protegge accidentally awakens Project: Shadow by placing a Chaos Emerald into a slot on the capsule it’s held in, and Shadow the Hedgehog awakens. Eggman, in a state of panic and confusion (he thinks it’s Sonic) tells Metal to attack, but Shadow defeats Metal and states who he is. He tells Eggman that in return for the Chaos Emeralds, he will grant Robotnik a wish. Eggman, of course, wants world conquest. Shadow tells Eggman to meet him on Space Colony ARK, and teleports away using the Chaos Emerald.
In the middle of the night, Shadow breaks into the Federal Reserve Bank and steals a Chaos Emerald.
The police are unable to identify the thief, but suspect Sonic thanks to the thief’s incredible speed, shape and Sonic’s past connection to the Chaos Emeralds. GUN kidnaps Sonic in the middle of the night.
Rouge the Bat decides to use her legal leeway to get into Eggman’s ranks by stealing an incredible gift - a treasure Eggman has gone after before, but failed to obtain. Knuckles isn’t exactly a fan of Rouge stealing the Master Emerald, however, and fights her to protect it. Eggman decides to get involved, trying to take advantage of the chaos to steal the Emerald. Eggman recognises it as the Master Emerald - not the Chaos Emerald he had been searching for. In order to stop both Eggman and Rouge from stealing it, Knuckles is forced to shatter the Master Emerald. Eggman leaves for his main base as Knuckles and Rouge race to find the pieces of the Master Emerald first.
Sonic wakes up in a GUN helicopter above Station Square, where he takes out most of the GUN guards (while still in cuffs), breaks his shackles and escapes by using a loose plating of the ship as a snowboard.
Eggman enters his main base to find a news report about “Sonic” stealing a Chaos Emerald from the Federal Reserve Bank. Eggman deduces the true identity of the thief as Shadow. He then uses his Spatial Teleporter to send him to Space Colony ARK.
Sonic has his City Escape and takes down the GUN Mobile Unit B-6f Big Foot. Sonic then encounters Shadow for the first time, who uses Chaos Control to escape Sonic and leaving him to be recaptured by GUN. Sonic is then sent to Prison Island as a Maximum Security Prisoner.
Rouge the Bat encounters Protegge, Orbot and Cubot entering Eggman’s Pyramid Base, and manages to sneak inside. She then discovers the Spatial Teleporter and its destination of Space Colony ARK. She encounters someone inside the base, and hides. As it turns out, it’s Cloak. He spots her easily, and the two decide to team up, using the Spatial Teleporter to enter the ARK.
Eggman soon meets Shadow aboard the ARK, and Shadow shows off the Eclipse Cannon to the Doctor. Protegge and Metal Sonic (who went with Eggman) are immediately impressed, just as Robotnik, but Orbot and Cubot are frightened witless. Shadow’s show of the Eclipse Cannon and talk of its potential makes the Doctor immediately decide to gather the Emeralds and use the Eclipse Cannon to hold the world hostage. Rouge encounters them in the middle of this exchange, and enters the scene. Cloak goes elsewhere, vanishing from view before any of the villains can see him. Rouge offers Eggman a Chaos Emerald in exchange for allowing her to join the Doctor’s team and use the Chaos Radar the Doctor has developed in order to find more Chaos Emeralds.
Rouge uses her connections to get Commander Tower to drop secure information - the fact that three Chaos Emeralds are all being kept on Prison Island. Shadow, Eggman, Protegge, Metal Sonic and Rouge all arrive at Prison Island, and the Doctor forms a plan. Eggman, Protegge and Metal Sonic distract the guards with an all-out offensive assault while Shadow sneaks into the armory and plants a bomb and Rouge breaks into the Vault and retrieves the Chaos Emeralds.
On his way into the prison, Shadow is tackled by an ecstatic Amy Rose, who has confused him for Sonic. She quickly corrects this mistake, however, and Eggman holds Amy at gunpoint. Amy runs, and Protegge chases her down while the rest of the task force continues their mission.
Tails flies to Prison Island, unable to believe that Sonic is responsible like they say he is. Tails then notices Amy and Protegge, and swoops down to save his friend. Tails and Protegge battle, but Protegge calls off the battle when Eggman calls her to action. Protegge flies away, leaving Tails and Amy to charge Prison Island.
Rouge breaks into the Vault, stealing all three Chaos Emeralds. However, she gets trapped in the Vault.
Amy rose arrives in Sonic’s cell room, using a key card she got off of a guard to open Sonic’s cell… on the condition that he agrees to marry her, which Sonic flatly refuses to. Amy opens the door anyways, and tells Sonic about Eggman’s crew. When Sonic hears about Shadow, he grabs Amy and jets away to go find him.
GUN Mobile Unit R-1/A Flying Dog flies into the Vault, attacking Rouge. The treasure hunter takes down the mech, but that doesn’t help her, as the pilot’s escape route closes before Rouge can get through to follow. Rouge laments about this over the radio, and Shadow streaks off to find her.
In the woods outside the prison, Shadow and Sonic encounter each other once more. Sonic unaware of the ticking time bomb and Shadow in a hurry causes Sonic to be the instigator, but Shadow happily fights anyways. A combination Chaos Spear/Sonic Wind attack causes Chaos Spears to be sent flying in all directions, wearing out the two before it wears out and dissipates. Eggman tells Shadow to hurry and get off the island before it explodes, which Sonic hears. As Eggman, Protegge and Metal Sonic flee, Sonic races to find Amy and Tails while Shadow dashes off to save Rouge and the Chaos Emeralds.
With only seconds remaining, Shadow breaks into the vault and uses Chaos Control to teleport Rouge, the Emeralds and himself to safety. Likewise, Sonic grabs Amy and Tails and gets them onto the Tornado just in time to escape the island’s explosion.
During this time while everyone is gone, Cloak deactivates Orbot and Cubot and grabs the schematics of the ARK. He then uses the Spatial Teleporter to escape back to Mobius, hiding so that the returning Robotniks don’t notice him before leaving the base.
Arriving back at the ARK, Shadow and Eggman decide to host a demonstration of the power of the Eclipse Cannon with the six Emeralds they have. Eggman then makes a public announcement, proclaiming his superiority while using the Eclipse Cannon to blow up half of the moon. His demands are for all the powers of the world to surrender within 24 hours, lest he destroy the planet.
Sonic, Tails and Amy witness this act, and determine that the Doctor is using the Chaos Emeralds - they’re the only thing with the kind of power needed for an act like destroying half the moon. Tails reveals he has the last Chaos Emerald, and says he can use it to find Eggman. GUN arrives, and Sonic holds them off while Tails and Amy escape. Cloak appears, aiding in the battle much to Sonic’s surprise. He allows Sonic to follow the others, vanishing into the night.
Eggman’s threats fall on deaf ears, and the Doctor sends Rouge to take the last Chaos Emerald from Miles Prower. Rouge does report in to GUN before leaving, however, and Topaz delivers her progress report to Commander Tower.
Knuckles finds Tails and Amy planning their next move just as Sonic arrives. Tails determines that the Emeralds must have been taken off-planet, and Tails picks up a conversation between the President and Eggman. Tails and Sonic head off to intercept the transmission and get the Doctor’s location, crashing into the limousine and finding Eggman’s location aboard the ARK.
The heroes regroup, and Cloak tells them he knows where Eggman’s base is. The heroes break into the pyramid, and send Knuckles to look for the Master Key to the base. Knuckles finds it, but has to fight a ghost to get it. Protegge finds the group breaking in, and she sics the Egg Golem on them. Sonic, Tails, Amy, Knuckles and Cloak all team up to take out the Egg Golem. Protegge escapes, however, and blows up the Spatial Teleporter that Cloak used in the first place. The pyramid is then invaded by GUN, led by Topaz. The lieutenant allies with Sonic and crew (but not before getting an autograph from her favorite music artist K.T.E. Knuckles), helping them locate a space ship they use to fly up to the ARK.
...however, the ship bumps into an asteroid and the cargo bay flies open. The Master Emerald shards Knuckles had collected flew towards Space Colony ARK, and Knuckles accidentally sent the shuttle into a crash landing in a frenzy to get the shards back.
The group “lands” on the ARK relatively safely, and splits up into two teams. Sonic, Tails, Amy and Topaz take the Emeralds - Tails’ real one and his fake copy - and the schematics Cloak stole to go shut down the Eclipse Cannon while Knuckles and Cloak go to find the Master Emerald shards.
Rouge, under the pretense of using the ARK’s defenses to stop the invading parties, gets Eggman to spill the password to the ARK’s central computers. Rouge comes upon some shocking truths when the computer alerts Rouge that Master Emerald pieces have been scattered around the ARK. Rouge races off to collect them… and as soon as she leaves, Cloak drops into the room. Meanwhile, Eggman takes Protegge and Metal Sonic and goes to meet with Sonic’s team himself.
Rouge and Knuckles encounter each other on the outer perimeter, and battle. Knuckles wins, and Rouge almost falls into a pit of lava. She’s saved, however, by Knuckles. As thanks, Rouge leaves behind the shards of the Master Emerald she’s collected, and Knuckles reforms the Master Emerald at last.
Amy and Topaz are left behind by Sonic and Tails, and Eggman manages to find them. Metal Sonic knocks out Topaz before she can fully draw her gun, and Eggman holds Amy at gunpoint. Protegge traps Tails in a metal claw as he’s returning to the scene, and Sonic arrives just after. Eggman orders Sonic to slowly place the Chaos Emerald in the middle of the room, and Sonic walks into the center with the fake Emerald. Eggman activates a trap, locking Sonic in a sealed capsule with the fake Emerald. Tails lets slip that Sonic has the fake Emerald, just like Eggman predicted. Sonic tells Tails to handle things and to take care of Amy before Eggman jettisones the capsule into space. A few seconds later, it explodes.
Shadow watches Sonic’s capsule explode, unimpressed.
Amy faints in shock, and only Tails and the Robotniks are still left active. Oh, and Metal Sonic. Tails manages to shatter the claw he’s being held in and wreck Protegge and Eggman’s mechs. Metal catches Tails off-guard and is about to choke him to death when Topaz shoves a piece of metal from the claw straight through Metal’s torso. Eggman manages to steal the Chaos Emerald, and the Robotniks flee, managing to get through a closing door before Tails catches them or they’re hit by one of Topaz’s bullets.
Meanwhile, Knuckles is running through the halls to meet up with the others and encounters Cloak. The pair senses powerful Chaos energy, and all of a sudden Sonic teleports in. Sonic explains that he used the fake Emerald to activate Chaos Control and warp to safety. Sonic asks Knuckles to go back and look after Tails and Amy, and asks Cloak to stop Eggman from making it to the control room. Sonic races off to place the fake Emerald in the Eclipse Cannon.
Rouge arrives back at the Control Room and sends the data files from the ARK concerning Project: Shadow back to GUN on Mobius. Cloak enters the room, using one of the ARK’s teleporters. He deduces that Topaz isn’t the only GUN agent on the station, and decides to help preserve her cover. Shadow enters, so Cloak and Rouge have a mock fight scene and Cloak “escapes” with the transmission equipment. Rouge’s cover is preserved, and Shadow is none the wiser. Rouge does, however, confront Shadow about something - a discovery she made “during the attack” - the fact that there is a file on the Ultimate Lifeform, and the picture is NOT Shadow but a completely different creature. Before Shadow can respond, Eggman tells the two over the radio that someone is entering the Eclipse Cannon’s main chamber and Eggman is on his way with the last Chaos Emerald. Shadow heads to stop the intruder while Rouge goes to rendezvous with Eggman.
Eggman and Protegge are running to the control room, but are stopped by Cloak. The mysterious rogue attacks the two, but they are saved by Rouge. The two battle each other, but a sudden spike of Chaos Energy causes Cloak to back off and retreat.
Sonic and Shadow encounter each other on the way to the Space Colony ARK. After exchanging dialogue (c’mon, you know what they say here) the two battle across the ARK. The battle eventually arrives in the main control room, and Sonic notices the main control panel with the Chaos Emeralds just as Eggman arrives. Sonic throws the fake Emerald at the slot just as Eggman is about to insert the Chaos Emerald. One goes in, the other clatters to the ground.
As soon as the Emerald locks in, red warning lights flash all over the ARK. Eggman, Protegge, Sonic, Shadow and Rouge witness as Professor Gerald appears on screen in the form of a final video recording. Professor Gerald announces that the ARK will soon collide with Mobius, and the force of impact will exterminate almost all life on the planet. As this is announced, Shadow laughs evilly and teleports away.
Tails, Amy and Topaz meet up with Knuckles, also seeing the video. Cloak arrives, saying that according to his sources back on Earth they have less than an hour before doomsday. Topaz confirms the same readings with GUN. Sonic teleports in with Eggman, Protegge and Rouge. Cloak walks in as well, with Professor Gerald’s downloaded diary. Eggman reads it and discovers that the ARK was a military attack meant to prevent Project: Shadow from falling into the wrong hands that was covered up as an accident (something Topaz didn’t know and felt betrayed about), Maria’s death and connection to Shadow, and the Professor’s vengeful feelings towards the world. Sonic, Tails, Amy, Knuckles, Topaz, Eggman, Protegge and Rouge all agree that they need to team up to stop the ARK, and Cloak points out that the best way to do that is to shut down the Chaos Emeralds using the Master Emerald. So the team devises a plan, splitting up into groups.
Sonic, Knuckles and Protegge are to take the Master Emerald to the Chaos Emeralds’ location, using Protegge’s Egg Mobile to transport the Emerald while Knuckles activates the Emerald and Sonic takes out any foes encountered on the way. Tails and Rouge are to head to the Emergency Control Room and open the fastest route possible, while Eggman works on repairing Metal Sonic in case of an emergency situation and Cloak scouts the area ahead. Amy and Topaz are tasked with finding Shadow and either convincing him to help or getting him out of the way.
Rouge destroys a switch keeping the control room doors closed, and Sonic’s team enters the control room… just in time to see the Chaos Emeralds be sent down to the lower area of the ARK. Cloak arrives in the ARK Core just as the Chaos Emeralds are put into position around a makeshift Shrine Isle, but Cloak is unable to reach them due to a forcefield. He flips a switch, and Tails notices one of the red lights on the Emergency Control Room turn green.
Amy and Topaz find Shadow sulking in the Observation Room, and Amy and Topaz try to convince him to help. Topaz brings up Maria, and Shadow kicks her across the room. Amy gets in the way, asking Shadow what Maria really wanted.
Shadow’s full memory returns.
Tails locates three other switches that need to be flipped in order to access the ARK Core through the main doors (the Master Emerald wouldn’t fit through the air vents Cloak took). Sonic flips one in the control room, Rouge flips another in her area and Eggman and Metal Sonic break through a bunch of GUN Robots and Artificial Chaos in order to reach the last switch and flip it. Sonic’s team enters the ARK Core. The Biolizard appears, trying to stop them. Shadow appears, and battles it, giving Sonic, Knuckles, Protegge and Cloak time to get to the Chaos Emeralds.
Shadow defeats the Biolizard, and Knuckles uses the Master Emerald and Tikal’s Prayer to stop the Chaos Emeralds. The Biolizard, making a drastic move to complete Professor Gerald’s mission, uses Chaos Control and fuses itself to the ARK - using its own weight to continue the descent to Mobius. Shadow gives up, stating that there is no way to stop the ARK now. Sonic says he’s missing something - their seven trump cards, the Chaos Emeralds.
Sonic and Shadow transform into their Super Forms, taking on the Biolizard. They fight it all-out, eventually beating it with a Super version of their accidental fusion attack from back on Prison Island. Together, Sonic and Shadow use Chaos Control to teleport the ARK back into orbit. However, the Super energy is fading. They’re unable to make it back to the ARK with the Chaos Energy they have left, so Shadow makes a decision and returns Sonic to safety aboard the ARK with Chaos Control. Shadow falls back to Mobius, happy that he’ll finally be able to see Maria again.
Sonic returns to the ARK, and gathers with his friends. The heroes head out, leaving Eggman, Protegge, Metal Sonic and Rouge aboard the ARK, with Eggman and Sonic vowing that next time they meet they’re back to being enemies. Eggman’s forces leave right after Sonic, as the Doctor returns to work on his next plan.
Cloak says farewell as soon as they land, returning to parts unknown.
Topaz provides crucial testimony that results in Sonic’s acquittal for his supposed criminal actions. She then returns to work as a GUN agent, operating as Rouge’s correspondent.
Sonic, Tails and Amy return to the Mystic Ruins, where Uncle Chuck is relieved to see them back safe. The quartet celebrates with Chuck’s classic Chili Dogs.
Knuckles is convinced by the Chaotix to make a sequel album to Unknown from M.E. He agrees.
A week later, Knuckles Chaotix has made top charts again with the new album Live and Learn.
