In the second part of the alien spaceship, you have to do battle with the gold jetpack jumper.

How to Defeat the Gold Jet Jumper

Also known as the brown jet jumper, this boss will go side to side, then sometimes charge downward toward you while shooting many bullets. Jump away from the jetpack jumper and jump over its bullets. Hit it with the Laser Gun, Lightning Gun, or Super Nova, or if those are unavailable, hit it when it comes close on the tiles.

Moving On

When it's gone, don't bother going into the hidden room north of where you battled it. This room is empty due to a bug. Instead, go east to proceed to part 3 of the alien spaceship.