Hey there dude, so had a quick read through what you've got down so far and thought I'd try to assist. Not much to go off, but thats understandable with it just being a concept, so I'll kinda just rattle off some questions and thoughts
First off since its not stated or immediately obvious in the story itself, what kind of Genre and tone will this be? I'm envisioning a Shonen/action type story, with some hints of School style comedy.
I see kenshin asked the same question I thought, why does he need protecting and what makes him special? So due to his dreams/premonitions, he can use the Alien tech. But as for these aliens, why are they coming to Earth? Is there a specific reason, is the war literally just about killing/saving the MC, or are they just sorta swept up in it?
In regards to the war, what are you going to do? Massive scale battles of two armies or specialised individuals being sent to fight?