Characters Shadow the Hedgehog, the protagonist, was created fifty years before the game's events by
Professor Gerald Robotnik in an orbital military research
space colony known as the ARK. Robotnik was trying to unlock the secrets of eternal life on the government's orders and create the "Ultimate Life Form." To that end, Robotnik designed Shadow to harness the powers of the Chaos Emeralds. To his horror, Shadow witnessed GUN raid the ARK and shoot his best friend and granddaughter of Gerald,
Maria Robotnik, killing her. Shadow was presumed dead at the end of
Sonic Adventure 2 (2001), his first in-game appearance, but he returned to life in
Sonic Heroes (2003) and suffers
amnesia. The Guardian Units of Nations (GUN) is the military of Earth's government, the United Federation, and is directed by the GUN Commander, who harbors a personal hatred of Shadow. When completing "Hero" missions, Shadow usually helps GUN and heroic characters from the
Sonic series, including
Sonic,
Tails,
Knuckles,
Amy Rose,
Rouge,
E-123 Omega,
Vector,
Charmy, and
Espio. Their aim is to protect Earth from both Doctor Eggman and the Black Arms, an army of various related alien species that invade Earth from the Black Comet.
Black Doom, the leader of the Black Arms, sends an extension of himself called "Doom's Eye" to watch Shadow and help him complete missions. When completing "Dark" missions, Shadow helps either Black Doom or Doctor Eggman, each of whom wants the Chaos Emeralds for himself. In one "Hero" mission of Sky Troops, Shadow assists Doctor Eggman in battling the Black Arms.
Plot Shadow suffers from amnesia, only able to remember two things: his name and his attempt to escape the Space Colony ARK with his creator Gerald Robotnik's granddaughter
Maria, who was killed by GUN soldiers. While Shadow is trying to remember what happened in his past outside the city of Westopolis, an alien race called the Black Arms drops out of the sky and invades the city.
Black Doom, the Black Arms' leader, contacts Shadow and tells him of an old promise made to bring the Chaos Emeralds to him. Stunned that Black Doom knows his name, Shadow searches for the Chaos Emeralds to learn about his past. The game progresses through the Westopolis level and five more levels from the different paths Shadow may take. As missions are completed, Shadow learns more about his past and regains memories. He can choose to help Doctor Eggman, the Black Arms, or GUN and the series' heroic characters, or he can choose to help neither and keep the Chaos Emeralds for himself. The missions completed determine which one of ten possible endings will be seen after Shadow collects all the Chaos Emeralds and defeats one of the game's final bosses. The possible ending events range from helping the heroes destroy the Black Arms to planning to destroy the planet. Completing all ten endings unlocks the game's true ending. After collecting all the Chaos Emeralds, Black Doom uses Chaos Control to bring the Black Comet to the Earth's surface. Black Doom explains that the Black Arms intend to use humans as an energy source, and the Black Comet begins to release a nerve gas into the Earth's atmosphere that causes total paralysis to those who inhale it. Black Doom sends a swarm of Black Arms larvae to eat Sonic, his friends and Dr. Eggman once they become paralyzed by the gas. Immune to the paralysis, Shadow confronts Black Doom, who reveals Gerald had promised him the Chaos Emeralds to complete his plan in exchange for his blood, which Gerald used to create Shadow. He attempts to use this physical connection to mind control Shadow. The Chaotix discover and play a message Gerald recorded for Shadow, revealing he created the ARK's Eclipse Cannon to destroy the Black Comet as atonement for working with Black Doom, asking Shadow to stop the Black Arms. Shadow resists Black Doom's mind control, and Black Doom transforms into a giant beast form called Devil Doom; in response, Shadow uses the Chaos Emeralds to transform into Super Shadow and confronts Devil Doom. During the battle, Doctor Eggman confirms to Shadow that he is the original and not an android. Shadow kills Devil Doom and uses Chaos Control to teleport the Black Comet back into Earth's orbit, where he obliterates it using the Eclipse Cannon. His friends are elated, as are people at GUN headquarters. Shadow is then seen in the ARK's observation deck holding up a photograph of Maria and Gerald. Recalling Maria's last words to him, "Goodbye forever... Shadow the Hedgehog", Shadow discards the photograph and walks away. ==Development==