Hey there! I'll tweak the design a bit so it's easier to understand. After you kill the boss you'll get the temperature expansion in the tunnel that leads outside. That item unlocks the heat-proof expansion (the one that says that you need another item before),
The spark shot lets you ignite the TNT, and at the right end of Prometheus, you'll find some TNT that will lower the level, letting you enter your ship.
That's where it both saves your progress and go back to Vangelos and continue with the progress.
You gotta trust me and start exploring that dead-end I told you in Vangelos to unlock the cold-proof expansion, letting you explore the rest.
Hope it helps!