It sounds like you've thought a lot about the setup for your story, and now you need to think about the story itself.
Like it would probably be a good idea for either Stella or Kyle to be designated as the protagonist first so we know whose story we're following.
Once you pick a protagonist, you can think through what the "journey" of the story is in terms of what they go through:
If the protagonist is Kyle, it's the story of an ordinary teenager who suddenly has a cute alien girl living in his house and discovers that she's a deadly super-weapon, and how he manages to prevent this.
If the protagonist is Stella, it's the story of an alien girl who adjusts to life on earth, only to discover she's a superweapon designed to wipe out most of humanity and how deals with it.
Try to think about how you can make the characters go through growth and change by solving whatever the big problem is, and how the place they end up at by the end of the story will contrast where they started.