Sonic, who has a fake Chaos Emerald, makes it to the central control room. Amy gets kidnapped by Eggman and demands the last emerald in exchange.

He destroys the engine, so it's up to Sonic now. Meanwhile, in Space Colony ARK, Tails is heading for the engine of the Eclipse Cannon. He defeats Rouge and gets the rest of the Emerald. Knuckles jumps ship and lands on a small planet and finds the pieces he lost, leaving Sonic, Tails, and Amy screaming on the ship which then crash lands into the ARK. Knuckles thinking quickly takes control of the ship causing it to spin out of control. Sonic remarks that only the Master Emerald pieces were inside there. In all the excitement of the space ship, the cargo bay opens releasing the pieces of the Master Emerald Knuckles had collected. As soon as he is defeated, they blast off in the rocket. Eggman appears and summons the Egg Golem, which Sonic has to take care of. Knuckles defeats King Boom Boo, the king of ghosts. Knuckles then has to find three keys to get into the rocket room. Sonic breaks through the security system. Eggman's 'secret' base inside the pyramid. Sonic, Knuckles, Tails, and Amy then head for Dr. Tails chases down the President, then he and Sonic tell the President about the situation they are in. He later pops out of a manhole beside Tails, who is talking to Sonic and Amy over a phone on loudspeaker. Meanwhile, Knuckles finds the last three pieces he can find of the Master Emerald in the Aquatic Mine.

He eventually finds Sonic and escapes the military. He has to find Sonic, tell the President and escape the military all before it is too late. Later, Tails discovers Space Colony ARK and the massive power of the Eclipse Cannon. A timer on screen appears saying 24 hours until mass destruction. Suddenly half of ARK comes off, revealing a long pointer called the ' Eclipse Cannon' which shoots out a powerful beam and destroys half of the moon. When they get back, Eggman is on televisions everywhere and it is revealed he is being taped from a space-station named 'Space Colony, ARK'. Sonic soon discovers the jungle is going to explode and leaves just in time. Meanwhile, Sonic gets weary, jumps off the missile, and lands on a small island in a vast jungle. Knuckles leaves Pumpkin Hill, and heads for the Aquatic Mine. There he finds three more pieces of the Master Emerald. Knuckles leaves Wild Canyon, and heads for Pumpkin Hill. Then Amy frees Sonic from his cell, and Sonic escapes on a missile. The next day Miles 'Tails' Prower comes to Prison Island in search of Sonic, rescuing Amy Rose from Dr. Knuckles finds the first three pieces in Wild Canyon. Knuckles and Rouge have a hunt for the pieces of the Master Emerald. Eggman tries to steal the Master Emerald, but Knuckles stops him in his path by breaking the Master Emerald into pieces. Shadow proceeds to use the emerald to transport to a different location, and Sonic is arrested.ДЄt the same time, Knuckles the Echidna and a mysterious character named Rouge the Bat are fighting over who owns the Master Emerald. Sonic realizes that the military is mistaking him for Shadow. After he destroys a military mech, he encounters a near look-alike of himself named Shadow the Hedgehog who has stolen a Chaos Emerald from the bank a while earlier.

Suddenly the pilot starts shouting 'What?! The hedgehog is gone! He's taking out everyone aboard!' At that moment, Sonic the Hedgehog jumps out of the helicopter, rips off a piece of the wing to use as a snowboard, and then jumps off. This story begins with a military helicopter (Sigma-Alpha 2) flying over the city with Sonic being captured aboard it. Spoiler warning: Plot, ending details or any kind of information follow.

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