A young man with no memory except for the last five years finds out he's an android sent to infiltrate the human race before the aliens arrive to take over earth. He must now save his new home from his own masters depsite just now starting to know his own powers.

Thanks for the feedback.

I've rewrote the logline like this:
A young amnisiac finds out he's a superpowered android sent to infiltrate earth before an alien invasion. He must now fight both the aliens and the distrusting military in order to save the world and his foster family.

I'm not sure about the last part if I should make the stakes character the family who took care of him when he crashed on earth or a human girl he fell in love with.

I think we have an overload of Inciting Incidents:

- he finds out he's an android
- the aliens arrive
- he finds out about his own powers

His main goal of saving his home probably goes further than that: he must save the world! We've just learned that aliens are taking over earth, so he'll have to stop the aliens.

I love the conflict that he'll be fighting against his own masters. But perhaps make the 'new home' somewhat more concrete... does he have a human wife? Child?

What are "his own powers"?

Currently it sounds like there is only going to be conflict between him and his peers, which makes Earth sound like completely disconnected. Think of JAWS and create a potential dilemma on earth as well. Once his cover is blown, they won't trust him, so there is your additional conflict. He's between two fires...

"A young man man discovers that he's an android sent to his now home planet, earth, to destroy the human race. He must now stop them, or lose everything that he loves."

Or something to that effect.This has the "or else factor" and invokes some sympathy for the main character I think.