OK, I got on the bridge and killed the Captain and his bridge crew. The other captives arrived and the other mothership starting attacking. After dieing numerous tims, running between the helm, the two generator buttons on the port side, and shooting other aliens somehow showing up on the bridge, everything is quiet.

Sally is standing looking at the locked door on the port side of the bridge. Paulson asked for some stimpacks, and is just walking around. Elliot Tercorian made me some Adapted Biogel, and says something about a jammer. He says "It's holding fine for now I guess. It should help with the bastards teleporting onto the ship.". I don't know if the samurai survived or not, I don't see his body. There are 11 alien bodies scattered around the bridge.

But the Death Ray will not fire. It says "the death ray is not ready to be fired". And the other ship is still out there.

I just found another generator button on the starboard side. The death ray still won't fire.

So what's wrong?

After the power goes out, did you push the 4 buttons needed to restore the power (to the death ray)?

And to the shields as well.

No. My error. I didn't see one of the buttons for some reason. The aliens are such gentlemen; waiting until your power is restored before blowing you to smithereens.