How did Megatron kill Mikaela?

Mikaela Banes, the human protagonist in the "Transformers" film series, was never killed by Megatron. In fact, he survives all three live-action movies, and even appears in the fourth film, "Transformers: Age of Extinction," despite his initial absence.

It's possible you're thinking of another character or story. There are many alternate continuities and fan fiction stories that could have different outcomes for Mikaela, but in the official live-action film canon, he remains alive throughout the series.