After Shadow either escapes the Death Ruins or Mad Matrix, or helps Eggman destroy all of the Temple Jewels in Sky Troops, Shadow comes out of Chaos Control in Iron Jungle and spots Sonic standing on the wing of Tails' new spacecraft. Sonic informs Shadow that the Black Arms are on their way to the ARK, and the black hedgehog agrees to follow them.
The player can either choose to help Doom's Eye destroy the six defense systems, attempt to beat Sonic in a race for the Chaos Emerald, or simply retrieve the Chaos Emerald normally.
Shadow Chaos Controls himself into an area based-around the Eclipse Cannon of the ARK, expressing frustration with the confusion of his memories. This however, puts him straight into a confrontation with the G.U.N. Commander, who reveals the reason for his antipathy against him as he witnessed the Ultimate Lifeform's creation by Gerald and Black Doom fifty years ago, along with his relationship with Maria. Shadow dodges a bullet from the Commander's gun, while the Commander himself questions if Shadow really did lose his memories. Shadow on the other hand promises to submit to justice if it turns out he really was responsible for the death of the ARK's population, walking away and leaving the Commander to question his own beliefs.
Shortly after starting the level, Shadow then notices the ARK's passageways collapsing all around him. After traversing through the debris, he eventually encounters Doom's Eye, who asks Shadow to retrieve a Chaos Emerald located in the ARK's power plant. As they enter the first interior area, Vector the Crocodile makes a surprise entrance, desperately searching for the ARK's computer room. The objective Shadow chooses ultimately depends on what actions the player takes in the final room of the power plant. Fall from the doorway to the floor and you'll be forced to complete the dark mission. However, you can also Triangle Jump across breakable panels or Light Dash to an elevated platform on the other side, from which you can traverse one more section of crumbling debris before finding the computer room and completing Cosmic Fall's heroic mission. Dr. Eggman pops up with his Egg Dealer, determined to stop Shadow from tarnishing his grandfather's legacy.
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