After you make it through the first part of the alien spaceship, you have to battle the Jetpack Jumpers.

How to Defeat the Jetpack Jumpers

Pick up the Anklet. Jump west and try to carefully use the laser gun to kill the Jetpack Jumpers while dodging their bullets. You can optionally kill the turret to have fewer bullets to dodge.

Get the First Magic Cube

When they're gone, go through the north door, then go north again to the next room. Go north, then go southeast and go down the southeast stairs. Follow the path and you will get the first Magic Cube. Your weapon will be upgraded to the Super Nova. You can only use the Super Nova if you have at least 11 full hearts. The Super Nova has a longer range than the Shooting Star.

Go north from there, and you will proceed to part 2 of the alien spaceship.