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After heeding Maria's plea and defeating the Artificial Chaos at Lost Impact, or beating Sonic the Hedgehog in a race for the cyan Chaos Emerald in Space Gadget, Shadow and Sonic are aboard the Space Colony ARK, and Sonic spots the Black Comet. Sonic fills in Shadow on what the Black Comet is, wondering if the Black Arms are somehow related to it. Shadow senses the presence of aliens aboard the comet and Sonic and Shadow then race off towards it, with them ending up using Tails' shuttle to fly across. Once aboard, Shadow can choose to either help Sonic find Black Doom at the core of the comet in his inner sanctum; as they follow his giant holographic broadcasts to hunt the alien prophet down, or aid Doom's Eye to fulfill a different mission - activate all four defensive shields to secure the comet against G.U.N.'s counterattack.
Dark: If Shadow chooses to aid Doom's Eye with sealing Black Doom's inner sanctum off from the impending counterattack by G.U.N., Sonic confronts Shadow alongside the G.U.N. Commander in the Diablon, shocked that Shadow would turn traitor when they had the Black Arms on their last legs, only for Shadow to reveal he only betrayed them in order to prove he was the stronger hedgehog in a final showdown with Sonic.
Hero: If Shadow chooses to aid Sonic in finding Black Doom, they confront the Black Arms' prophetic leader in his inner sanctum to stop his invasion once and for all as Shadow intends to keep his promise to Maria.
This section requires an expansion.
The following weapons can be found in Final Haunt:
Pass through the large loop after the third Save Point then, once at the room with the Black Oaks, go up the right ramp and destroy the rock to reveal the Key.
Don't activate the second shield switch, and instead just continue forward. The Key is located in the back-right corner of that room.
Activate the second shield upon reaching the area with the Cell Cannon, then look to the left.
Just after a Secret Door, Light Dash up to the next area and ride the platform to the path on the other side with the Key.
While many Secret Doors are present in this Stage, they all contain the same things: Cell Cannon turrets. The first two have the turrets right behind them with good cover to protect them from being destroyed by energy shots from the Black Arms' gun ships. The second two lead to springs that bounce up to where the turrets have been deployed for dealing with the gun ships that appear in that area.
Because the stage is swarming with Black Arms, filling up the Hero Gauge should be simple. In fact, some rooms need to be cleared of Black Arms before Shadow can even continue. Do not hit any of the shield switches, as this will block off the Goal Ring and force the player to double-back to shut them back off. Use nearby Vacuum Pods to pull blocks out of the walls and stop lasers.
Many parts of Black Comet and The Last Way are identical to Final Haunt, with the former flooded with toxic liquid and the latter having some of its doors inaccessible and requiring the use of Chaos Control.
When Sonic meets Shadow in this Stage, he says "Well, Shadow, looks like we've reached the climax of this little game." but the subtitles read: "Well, Shadow, looks like we've reached the climax of our little game."
When the player gets to the Red Slime, both Doom's Eye and the subtitles incorrectly say to "get in." Sonic also says "get in," but the subtitles for him correctly say "on."
Completing the Dark mission grants the player an ending that is considered a Dark ending despite being on the Pure Hero route. This is the only level in the game where the player can get an ending that has a different morality then the route they were on.