If you are having trouble beating Megatron X, press c-right rapidly to get him down on the ground. Then, while he is down, charge and ultra shot. Get it as charged as much as possible before Megatron X can recover. Blast him! Repeat. Your energon bar should go out soon. Transform to beast mode and keep hitting him rapidly. Once your bar is full, transform and repeat the process.
Playing as Megatron, successfully complete the game with no time limit. At the end of the game you must fight Megatron X.
Simply complete the entire game including defeating Megatron X. You will get Rattrap's armor from the first episodes.
For the following secret characters, first select either arcade or versus mode. After highlighting the corresponding character (in italics below), hold Z and then select the character with the A button. While you press left or right to view his various colors, the hidden character will be selectable:
Ravage and Tigatron - Highlight Cheetor
Starscream - Highlight Waspinator
Blackarachnia - Highlight Tarantulas