I know the details of the book well enough, but I can't remember the title or series title for the life of me. It is recent (Post 2008 or so). YA sci-fi. Set in the UK at modern times.
Book one, kid skulks around London, hiding. Aliens have completely taken over the world by broadcasting a signal that "reprogrammed" the humans to do slave labor. Two creatures took care of the humans, the hunters (floating maintenance drones with a poisonous stinger) and giant assault humanoids (that turn out to be automated exoskeletons).
Main character was given injection of nanites by secretly adoptive father (who is an alien) that enables the kid to resist the signal. He gets stung, and is found by a group of militant kids who take him to their base to see if they can help/if he will survive. He does, they train, and find the aliens have drilled a hole into the earth's core.
They take the fight to the mothership with a can of fabricated nanites originally taken from the main character (who has them floating in his body). Alien mastermind turns out to be a intelligent swarm of nanites. The main character shoves the nanites into the swarm, losing his hand in the process, and turning the nanite AI into a friendly golden figure. The figure refers to him as Illuminant.
Book two, Essentially this, boy finds his father, finds the father is an illuminant (alien) scientist, and a military dude from another shielded base is a warrior-caste Illuminant.
The Illuminants are revealed to be composed of nanites after 'transcending' their physical form. While an enemy mothership moves from another country to attack the friendly mothership, they find some humans have been super-mutated into crazy monsters, and one semi-mutated girl, Maggie(?) is the only friendly one. The warrior-caste illuminant kills the dad, takes over the friendly mothership, and plans to infect all humans with his bio-weapon (which created the super-powerful mutants) in an attempt to destroy the enemy motherships. The history of the Illuminant was revealed, and why the motherships are trying to drill to the earth's core.
The kid is turned into an illuminant and can turn into a swarm of nanites. At the end, the warrior-illuminant is defeated along with the enemy mothership (which is turned into a golden, friendly ship) and a giant father-of-all-behemoth ships comes into the solar system (and it is revealed that it is a corrupted illuminant sent to travel the stars).