The Mechs attack on the season finale, but Scott and Ben are able to find a frequency that messes up their communication. They retreat as a result, leaving the road clear.
Tom uses this to his advantage, riding into town to help with the attack on the structure (and kissing Anne goodbye in case anything happens to him, as she's now in charge of the survivors being funneled out of the school). When he arrives, he finds most of the resistance force dead. But he does locate Weaver.
Inspired, Tom uses a bazooka to shoot down an alien ship, which then crashes into the structure and starts a major fire/explosion.
As Weaver and Tom head back to the school, they are approached by a harnessed Karen. She introduces one of the alien leader, a non-Skitter and non-Mech. Talking for him/through him, she asks that Tom agree to speak with the being and uses Ben as bait. Can the aliens save Tom's son from becoming one of them?
Holding on to that hope, he walks into their space ship right before the credits roll.