Flashback from 50 years ago before Shadow was locked up. His back story is that a meteorite containing the alien hedgehog Shadow crash-lands in Oklahoma and is seized by the U.S. military.
Shadow's power was experimented on by Professor Gerald Robotnik at a Guardian Units of Nations (G.U.N.) research facility under the supervision of Captain Walters.
He also developed a close friendship with Maria, who found him in one of the laboratories and turned out she was Gerald's granddaughter.
One night, Gerald, Maria, and Shadow try to escape the facility to prevent Shadow from being taken away.
Captain Walters was the only one that tried to protect them saying that they were just kids and they shouldn't shoot on them, however they didn't listen.
And while he was trying to stop them, one of them accidentally shot in one of the fuel tanks leading to an explosion in which Maria didn't make it.
Walters shuts down the facility, imprisons Gerald, and places Shadow in suspended animation.
Back in nowadays, fifty years later something goes wrong. Shadow has been released and he's seeking his revenge for what they did to his only friend.
The question is, did Maria really died back in the explosion or is there something else beneath the surface?