Evertime I play the allies they use these two weapons one is a missle and it creates alot of damages and the one other is this bomb that just appears. I try to be the allies and use these weapons but I do not seem able to.Can you defend against these two weapons?

You are talking about the Top Secret Protocals, the Surgical Strike and the Time Bomb. Yes, there is a way to avoid them, order your units to move out of the way of the radius of those weapons, but if it appears on your base you can either destroy it or just repair or replace your damaged or lost structures.

Dont shoot at the bomb, it just makes it blow up faster.