Megatron will only take 1pt damage from any single attack. He's also assisted by Decepticon Brawlers who have an annoying habit of healing him. Focus you squad's attacks on Megatron, move only as far as you need to get him in range and use 1AP attacks as anything above that is a waste. By conserving AP you'll build you Energon meter which will allow you to use a bonus attack for one (or two) of your characters. Again, use the lower powered version of the Ultimate as it will only take a single point off Megatron either way and that will leave you enough Energon to pull the same trick again inside that round.
If you attamept all this on easy then you shouldn't have to worry too much about his goons doing too much damage to your squad. One Autobot must survive till the end of round five to complete the mission but this achievement isn't tied to that, once Megatron has lost 50% of his health the achievement will pop.