Captain owed pirates money he borrowed previously.
A bright light can hollow the deepest of nothingness.

Everybody is asking the wrong question, remember the captain's cabin scene when he's about to commit suicide after losing his cargo in the storm. For some reason he needed money desperately enough to risk everything, including the lives of him and his shipmates, even try to bargain with the alien for a chance to salvage the ship. Was it ever hinted in the movie why he needed the money so much.

If he was smart he probably had given up on the idea of keeping the ship for salvage by then. I thought at this point he was only bargaining for his life. And it seems like the alien held up its end in a way by letting him keep his mind and control of his cyborg body. In any case, he really didn't seem too upset when he confronted his crew.

Yeah, this would be among my biggest peeves with this flick.
Just what motivated the captain to arrange a deal with an alien intelligence to have him mutilated into a bionic freak? Did he think his chances of claiming the ship's salvage went up? Or maybe he's especially sensitive to punches in the face? What the beep.

This movie was bad enough without a needless spoiler. Good job.
Don't trust reality. After all, it's only a collective hunch.