There is a bug in the programming. During the 1st battle with Brainiac you will be able to destroy only 3 of the 4 electric towers and for the 4th there will be a perpetual loop.
The solution: Exit the game and restart from the last save point, this time all 4 electric towers' protective covers will be down one at a time. After these are destroyed it is a cake walk killing Brainiac twice. However there is a twist in the tale, kill Brainiac and discover the story for yourself.
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It is spelled "Egg Emperor" and you have to keep using Thunder Shoot to beat it.
beat the game? lol
Beat all the turtles.
Go fast and dont die
You beat heroes mode on story