What should have happened is the remaining twin gets enraged and starts to firing homing rockets. You would have to then dodge these rockets in such a way that they come back towards the Twin and hit him, resulting in another "power downed" stage where you can attack him. Of course, the rockets would have slightly adjusted targeting AI so that it would be easier to hit one of the Twins.
Course, other ideas could work (I'd be happy to hear suggestions). Im just saying that the ending was kinda lame. The boss fight was awesome overall though.
the boss is challenge enough i count my blessing just beating it