What is the missile silo and how do I power it?

I had been thinking the same thing; what good is this missile silo, and how do I make it work?

Warning, spoilers ahead.

It comes at the end of the second part, after you collect all the DNA fragments and make it back to sector seven one last time. There, Admiral Born has had it with you, and attacks you with his fleet capital ship. The only way to win is to pull energy cores from the turrets and deliver them to the missile silo. Its a bit of a game of chicken, as getting caught in the open when his particle beam is charged is instant death. So you have to get cores, hide behind mountains, and make a mad dash through enemy craft and laser fire to deliver the core to the silo. Several times.