This is the 5th Boss in Captain Commander, that unfortunately did not make it into the game.  

The game turned out to be more complex than we imagined (surprise!) so we had to cut the final two levels. Escape from the alien planet (level 6 - See image here) & survive the descent back down to the surface of Earth (level 7 - we had just started designing this one).

Basically, Captain Commander defeats the Mother Brain, gets all the rescued humans into a space-faring vessel (kinda packing in clown-car style ;), & escape the planet, piloting his way through the alien defenses & space junk, reaching the large 3-piece orbiting Boss.  He needed to survive while destroying the shield generator & them jump to FTL speed back to earth.

Once he reaches Earth, since he’s in an alien ship, the Earth military attacks full force.  He was to dodge and weave his way down to the surface, where they would finally recognize it was him in the ship.  (I guess the Alien ship’s comm-system was busted in the dramatic escape from the planet).

End cut-scene: would have been Captain Commander landing safely with happy banter between he and the earth military commanders, and the rescued scientists all leaping out of the small alien ship,(again clown car style ;)

The end. or is it.. ??