As Shadow seizes the fifth Chaos Emerald, his fractured memory is starting to come together again. Shadow remembers the fatal fall out of orbit after killing the Finalhazard; waking up in a vat of green goo inside an Eggman base and row upon row of other Shadow Androids, stored neatly in their own capsules. Combined with Eggman's devious insinuations through the previous course of the game, Shadow comes to a final conclusion: that he is a Shadow Android, an Eggman-made copy of the deceased original Shadow. Determined to kill his creator, the hedgehog races towards the doctor's base.
Circumstances, however, do not make things easy for Shadow. In Iron Jungle, despite most of their forces fighting in their war against the Black Arms; G.U.N. has mustered the vast firepower and resources necessary to assault the Eggman Empire. Eggman retreats into a classic supervillain active volcano hideout. Indeed, the only participant of GUN's attack to even make it inside Lava Shelter is E-123 Omega, who asks Shadow for assistance in breaking through to the fat scientist at the base's core. Alternatively, Shadow can slow the G.U.N. forces down by activating the base's defenses, ensuring that his confrontation with Eggman won't be disturbed by the humans.
No matter which route Shadow takes to his final confrontation with Eggman at the base's core, it ends with Eggman facing Shadow in the Egg Dealer with Omega supporting Shadow during the fight.
The following weapons can be found in Lava Shelter:
You need to shoot the defense systems three times to activate them, unless you use the Shadow Rifle, in which case you only need to shoot it once to activate it. Triangle jump in the area past the third checkpoint to move faster.
A Black Arms' Air Saucer and a lava path, the saucer makes it possible to cross the lava and therefore collect all the items, which include Rings, lives and a heal unit for the vehicle. There are two Lava filled Paths that cannot be crossed without the Air Saucer. This also makes it easier to traverse in the dark mission where the lava level will rise upon activating a generator.
All of Dr. Eggman's voice clips that are exclusive to this stage were left raw, instead of being edited to make them sound like he's using his Egg Monitor to talk to Shadow. The ones that weren't left raw are those common to all levels where Eggman's Drone appears as an ally (for example, those where he criticizes Shadow for attacking his robots).
This is the only final stage in the game that has the same boss for both Hero and Dark missions.
Omega will also still be Shadow's partner during the boss after completing the dark mission, despite not appearing in the cutscene prior or after the fight.
At the beginning of the stage Shadow says "I'll make you wish you'd never created me!" but the subtitles read "I'll make you wish that you'd never created me!"
Despite the fact that Eggman says that GUN are surrounding his base, GUN robots are nowhere to be seen in the stage.