In a patch of space, mostly empty, a portal appears and the Interceptor II comes out. As the portal is closing, a blast of flame shoots from it. The Interceptor II's dimensional transporters are fused in that blast, too badly to be repaired and stuck in too badly to be replaced. So, it looks like the Interceptor II will be stranded for a while, expecially considering this area of space is out of Xion's survalience grid, and too far away for telepathic communication.

A galaxy away, a fleet can be seen. Composed almost entirely of transports, the fleet is in sorry shape. It is near a star system with only one hospitible planet, and no intelligent life. Aboard the fleet's flagship, the Black Arbiter, a tall, greyish-skinned being shakes hands with the general of the Peep Army, with his right-hand man in the background. The imaginary point of view pulls back, and begins to fade.

Part Three- New Beginnings

Note- you have no control over where the portal sends you. After you destroy the computer you can not longer program the portal, and before that the computer was still locked down. It just quickly changed it's end point before you destroyed it.