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 Space Colony ARK, and Sonic spots the Black Comet. Sonic fills in Shadow on what the Black Comet is and wonders if the Black Creatures are somehow related to the Comet. Shadow senses the presence of aliens aboard the Comet and then Sonic and Shadow race to the Comet. Shadow and Sonic apparently used Tails' shuttle to fly across. Once aboard, the player 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.
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. 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.
The following weapons can be found in Final Haunt:
In this level there are quite a few secret doors however, behind all the doors are the same objects: Cell Cannon turrets. The first two have the turrets right behind them, with good cover to protect them from being destroyed by the 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 gunships that appear in that area.
This is only stage where players do not need a time bonus to get an A rank for the Hero mission, provided you kill every Black Arms soldier/gunship you can find.
Many parts of the stages 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 requiring the use of Chaos Control.
When Sonic meets Shadow, 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, Doom's Eye and the subtitles incorrectly say to "get in" while Sonic also incorrectly says "get in" but the subtitles 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 shown by the game playing the Evil Ending theme during Shadow's final speech. This is the only level in the game where the player can get an ending that has a different morality then the route they are on.