How did Megatron come back?

Answer 1

because the all spark is full of raw power when they put a tiny piece left from the first movie in him he came back and since he was already evil it didnt effect him anymore than that

Answer 2

The piece of the Allspark is stollen from NEST by the Decepticons and they go to where Megatron is, at the bottom of the Abyss, and they stick the shard in his chest.

Answer 3

The constructicons and Ze Doctor go to the botom of the ocean and bring him back to life