Sonic Adventure 2 is split in three stories - Hero (Sonic the Hedgehog, Knuckles the Echidna, and Miles "Tails" Prower in his "Cyclone" mech), Dark (Shadow the Hedgehog, Rouge the Bat, and Dr. Ivo "Eggman" Robotnik in his Egg Walker mech), and the Last Story, unlocked through beating the first two.
Meanwhile at a desert, Knuckles the Echidna and new character Rouge the Bat are fighting over the Master Emerald. Dr. Eggman tries to steal the Master Emerald, but Knuckles stops him by breaking the Master Emerald into pieces, which made Rouge angry with him over it. With Eggman leaving, Knuckles and Rouge have a hunt for the pieces of the Master Emerald like the former did previously. Knuckles finds the first three pieces in Wild Canyon.
The next day, Miles "Tails" Prower flies to Prison Island, a reinforced base owned by G.U.N., in search of Sonic. He finds Amy Rose being cornered by Dr. Eggman and has his Tornado-2 transform into the Cyclone to defeat Eggman's walker. Amy reveals she came to save her hero, Sonic (again), and Tails infiltrates Prison Lane to lead Amy to Sonic. Then Amy frees Sonic from his cell, and Sonic heads out to Metal Harbor. He lands on a small island in a jungle in where he confronts Shadow once again and the two duke it out. He soon discovers the island is going to explode and zooms through Green Forest, leaving the island with Tails and Amy just in time.
Meanwhile, Knuckles arrives in Pumpkin Hill, a haunted area full of mountains shaped with a pumpkin faces. There he finds three more pieces of the Master Emerald.
When Sonic, Tails, and Amy get back to Central City, Eggman is on televisions everywhere and it is revealed he is being taped from a space-station named the "Space Colony ARK". Suddenly half of ARK comes off, revealing a long pointer called the 'Eclipse Cannon' which shoots out a powerful beam that destroys half of the moon as a demonstration. A timer on screen appears, signifying 24 hours until mass destruction. Tails is in possession of a Chaos Emerald and says he can use it to detect Eggman's location, but the police surrounds the heroes, which leads to them escaping from them in Mission Street.
Meanwhile, Knuckles finds the last three pieces he can find of the Master Emerald in the Aquatic Mine. He later pops out of a manhole beside Tails, who is talking to Sonic and Amy over a phone on loudspeaker. Tails can't detect the rest of the Chaos Emeralds anywhere, so he assumes Eggman somehow took them to outer space, and he plans on finding the President and finally locating Eggman's whereabouts. Tails chases down the President at Route 101. Sonic and Tails get inside the President's limousine and discovers that Eggman is at the Space Colony ARK.
Sonic, Tails, Knuckles, and Amy head for Dr. Eggman's "secret" base inside the pyramid. Tails gets through Hidden Base while Sonic runs down to Pyramid Cave in where they approach the center of the base. They realize they need a key to go inside; Sonic volunteers Knuckles to go and find three keys to get into the rocket room. After Knuckles finds the three keys in the Death Chamber, he encounters King Boom Boo, the king of ghosts. He defeats the giant ghost and finally the door to the center is unlocked. After that, Dr. Eggman appears and summons the Egg Golem, which Sonic battles and defeats. As soon as he is defeated, they blast off in the rocket.
In all the excitement of the space ship, the cargo bay opens releasing the pieces of the Master Emerald Knuckles had collected. Sonic remarks that only the Master Emerald pieces were inside there. Thinking quickly, Knuckles takes control of the ship causing it to spin out of control. Knuckles jumps ship and lands on a small planet to find the pieces he lost, leaving Sonic, Tails, and Amy screaming on the ship which then crash lands into the ARK. Sonic, Tails, and Amy enter inside the ARK. Tails brings out a fake Chaos Emerald in which has the same wavelength and properties as the real Emerald. He plans to destroy the Eclipse Cannon's generator while Sonic use the fake Emerald to sabotage the Eclipse Cannon's firing. Tails goes through Eternal Engine and destroys the engine, so it's up to Sonic to put the fake Chaos Emerald with the rest of the 6. However, Amy gets kidnapped by Eggman and demands Sonic to promptly arrive to the research facility room.
Meanwhile, Knuckles finds the rest of the Master Emerald shards in Meteor Herd and encounters Rouge and the two treasure hunters engage in a battle. The two start arguing until Rouge falls off a bridge. Knuckles saves her from falling down the lava. The two gaze at each other until Rouge snatches her hand off of Knuckles, and the two argue again. Knuckles claims that he was saving the pieces of the Master Emerald, which prompts Rouge to give him the rest of the pieces, albeit reluctantly. Knuckles restores the pieces of the Master Emerald and apologizes to Rouge for hurting her, and leaves.
After getting through Crazy Gadget, Sonic arrives to the research facility room. Eggman anticipated the likelihood that one of them had the fake emerald, and after tricking Tails into admitting that Sonic had the fake emerald, Eggman then shot Sonic out of an escape capsule that was going to explode in the middle of space. Before being launched out, Sonic encourages Tails to stop Eggman, and tells Amy to take care of herself. Just before the pod exploded, Sonic also considered the possibility of using the fake Chaos Emerald to escape via Chaos Control, after remembering that it has the same properties of the real one. All Tails, Amy and Eggman can see is a capsule blowing up, so they presume Sonic was killed in the vicinity. Tails is so angered by this, and inspired by his supposed final words, he defeats the Doctor.
Meanwhile, Knuckles spots Sonic coming out of a portal. Sonic tells Knuckles that he managed to use Chaos Control to save himself and asks him to help Tails and Amy. Because there isn't much time left, Sonic makes his Final Rush to outer area of the ARK to reach the Eclipse Cannon. Sonic confronts Shadow one last time and defeats him.
Tails, grieving over Sonic's "death", attempted to tell Sonic that he managed to defeat Eggman. As Eggman slowly snatches the last Chaos Emerald, Sonic, having apparently overheard Tails' comment, responds by congratulating him, causing Tails and Amy to learn that Sonic survived from the exploding capsule. Sonic then told them to look outside. They then look out the window and sees that the Eclipse Cannon is exploding before it could fire. The scene ends with Sonic at the tip of the cannon smiling with his thumbs up.
Meanwhile, Rouge the Bat is fighting with Knuckles over Master Emerald. Dr. Eggman uses this to his advantage, and attempts to take the Master Emerald. Knuckles stops him by breaking the Master Emerald into pieces. Rouge and Knuckles have to hunt for the pieces of the Master Emerald. Rouge finds three pieces in Dry Lagoon.
Later that night, Dr. Eggman goes to his pyramid base through the Sand Ocean to check up on things, and watch the replay of the news. He finds out that the G.U.N. robots are guarding his pyramid base. He destroys them and goes on inside. While he is watching the replay of the news, he discovers that Shadow had stolen a Chaos Emerald from the Federal Reserve Bank yesterday with everyone mistaking him for Sonic. The scene changes to where Shadow is leaving the bank when he has a flashback of what happened on Space Colony ARK with him and his friend Maria Robotnik, promising her revenge afterwards. He proceeds to speed down the highway, destroying any robot that gets in his way. He later sees Sonic, explains to Sonic who he is and leaves.
The next day Rouge, actually a spy for G.U.N., infiltrates Dr. Eggman's base. To do so, she has to find three keys in the Egg Quarters. After finding them, Rouge is teleported to the Space Colony ARK. Meanwhile, Dr. Eggman goes through the Lost Colony and finds Shadow on board the ARK, near the control room in question. Shadow tells Eggman about Space Colony ARK and the power of the Eclipse Cannon, which is capable of destroying an entire planet. He then puts in the two Chaos Emeralds and tells Eggman that once all seven Emeralds are collected, he will use the Eclipse Cannon any time he wants and then the world will be conquered. Rouge interrupts the conversation between the two, and persuades her conditions to Eggman into helping her by giving him a Chaos Emerald, and telling him where three other emeralds were.
Shadow, Dr. Eggman, and Rouge arrive at Prison Island, where the three Chaos Emeralds are located. Dr. Eggman breaks through the Weapons Bed, and before the team continue, Amy arrives and hugs Shadow whom she believes is Sonic until she quickly realizes her mistake. Eggman threatens Amy until Tails makes the save. Tails and Eggman battle in their mechs with Eggman winning the battle.
In the Security Hall, Rouge finds the three Chaos Emeralds and defeats another military robot, "Flying Dog". However, the fight leaves her locked inside the room. She contacts Shadow about her predicament, to which he has a flashback of Maria and goes to save her. Shadow rushes through White Jungle, plants the bomb, finds Sonic and fights him. It ends in a tie, neither of them win because Shadow has to escape the jungle before it blows up. So he rescues Rouge, and warps onto the ARK.
Shadow was having a flashback on his past with Maria until Rouge interrupts, mentioning how it was unlike of him to save her life. Shadow claims that he only came for the Chaos Emeralds. Later, Eggman is broadcasted on the televisions everywhere and it is revealed to all he is being taped from the ARK. Half of the station comes off, which reveals the Eclipse Cannon and shoots out a powerful beam, destroying half of the moon. Then, there is a timer on the screen, signifying 24 hours until mass destruction. At the ARK, Rouge explains that she knows where the location of the last Chaos Emerald is: with Tails, having received it as a reward for saving Station Square from Eggman's missile. Shadow and Rouge try to catch the Tornado. Rouge chases down the bioplane in her car in Route 280 and Shadow can't catch them in Sky Rail. Eggman tells Shadow that he'll give the heroes a warm welcome.
By this time, Knuckles has unlocked the center of Eggman's base, so Eggman summons his Egg Golem. However, Sonic damages the restraining mechanism on top of its head, causing it to turn on Eggman, so Eggman has to destroy his Egg Golem, but unfortunately the heroes manage to leave in their shuttle. Rouge soon discovers that Knuckles is on a small planet with the pieces of the Master Emerald. She finds half of the pieces in Mad Space, then they fight. It is a draw and she gives the pieces to Knuckles.
A while later inside the pyramid, he and Shadow discover that Sonic and his friends are on the ARK and Eggman seeks to confront them. Eggman discovers that they have a fake Chaos Emerald, and goes to intercept them through the Cosmic Wall. Eggman then kidnaps Amy and orders her to tell him where Sonic and Tails are. Tails eventually gets there while Sonic rushes into the room he was in. Eggman shoots Sonic out of an escape capsule which is going to explode, and then he defeats Tails, despite the young fox's best efforts, and takes the real Chaos Emerald. Meanwhile, Shadow witnesses the "death" of Sonic, saying that he was just a regular hedgehog after all. He then spots Rouge attempting to take the other six Emeralds and exposes her as a government agent. Rouge then proceeds to show him the results of Project Shadow, with the picture showing an entirely different being. She then questions Shadow that is he really the Ultimate Life Form or not. Eggman contacts Shadow, declaring that someone is attempting to get to the Eclipse Cannon and orders him to stop them before the cannon fires again. Shadow makes a Final Chase to the cannon and finds the culprit to be none other than Sonic, who survived the capsule explosion. The two hedgehogs battle for the last time and Shadow wins.
Meanwhile, Eggman is putting in the last Chaos Emerald. While he is cheering over his accomplishment in conquering the world, a nearby monitor turns on forebodingly.
Meanwhile, it continues from the Hero Story, where Sonic and Knuckles enter the room Amy and Tails are in, but then they hear a rattle and suddenly Rouge comes out of the blue. She informs that they are all doomed because the Space Colony ARK is heading towards Earth at a tremendous velocity. On televisions everywhere, including the ARK, Gerald Robotnik is tied to a seat, explaining how the ARK will crash into Earth and destroy it along with the savage humans, with the power of all seven Chaos Emeralds.
Eggman comes in and Knuckles berates him, thinking that he was behind all of this. Eggman then scowls at Sonic for surviving the capsule explosion, and then gives Rouge his grandfather's diary and Rouge reads it out loud, 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 insane because he loved Maria so much, and was devastated that his own research led to her death. He wanted revenge on all humanity, so he created the Eclipse Cannon while still working under G.U.N. and programmed it such that once the seven Chaos Emeralds were inserted, the ARK would fall to Earth. It is revealed that Gerald made Shadow to benefit mankind, but Space Colony ARK was destroyed and 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.".
Both the Hero and Dark characters (with the exception of Shadow) put aside their differences and plan to stop the energy of the Chaos Emeralds to stop Space Colony ARK from crashing with Earth in the Cannon's Core. They have a plan to stop the Chaos Emeralds with the Master Emerald, which Knuckles mentioned can neutralize the emeralds. Meanwhile, Amy finds Shadow and convinces him to help save the world. Shadow refuses, declaring that it's all going according to plan, to which Amy says that even though there are selfish people like Gerald said, there are still good people down there. He then receives a flashback of Maria, in her dying words, telling Shadow to give humanity a chance to be happy. With a tear in his eye, Shadow realizes Maria's true request and takes off to the Cannon's Core.
Sonic and Knuckles are seen at a shrine that looks somewhat like the Emerald shrine of the Master Emerald at Angel Island. When they try to get closer to the shrine to stop the Chaos Emeralds with the Master Emerald, Gerald's voice is heard again and a lizard like beast called the Biolizard is awakened. They realize that this is the prototype of the Ultimate Life Form, initially sealed away and used as a scapegoat for the supposed "accident" on the ARK. Shadow appears and battles the Biolizard, while Sonic and Knuckles get to the shrine and find a space for the Master Emerald. With the Biolizard defeated, Knuckles does the chant to negate the power of the Chaos Emeralds and the Biolizard disappears. Eggman informs the three that the Biolizard is still alive as it used Chaos Control to teleport and fuse together with Space Colony ARK to become the FinalHazard and is keeping it on its crash course to Earth.
With the Space Colony ARK no longer being powered by the Chaos Emeralds, but now by the FinalHazard, Sonic and Shadow use the Chaos Emeralds to transform into Super Sonic and Super Shadow. They defeat the FinalHazard in outer space, with Shadow slowly losing energy throughout the fight. Just as they are about to stop Space Colony ARK's descent, Maria's voice rings in Shadow's head again about giving people a chance to be happy. Both Sonic and Shadow used a super-powered Chaos Control to warp the crashing space colony ARK back to its normal place. Shadow's power is drained, and falls down to earth, realizing that he has fulfilled Maria's request in his "dying" moments.
Sonic returns to the ARK alone, giving Rouge Shadow's ring cuff and everyone reflects on the events that have transpired, wondering what they will do next as the credits roll. Eggman discusses to Tails about Gerald Robotnik, saying that he looked up to him as a child, and was shocked that he would destroy the world. Tails brightly says that they all saved it together. Knuckles asks Rouge what's next for her, to which she replies that she will stop looking for jewels and is thinking of something better than them. As Sonic and his friends leave to return to Earth, Sonic quietly bids his farewell to Shadow the Hedgehog in the same manner as Maria.
