In the last scene of the series we see Will and Beanpole return to the rebel's base camp and are devestated to find it abandoned. However they are then joined by the other teenagers they have rescued suggesting that they are going to restart the human resistance movement from scratch. In the books we learn that the rebels moved camp as a security measure and send scouts to bring the group to the new base.
In the third book of the series the human rebels destroy the alien cities on Earth freeing the population who have been 'capped'. Humanity begins to live without alien influence and nations immediately begin bickering with one another. The three heroes therefore vow to work to make humans live in peace together.