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Falling Skies jumps ahead three months and gives us an idea of what Tom went through on that alien spaceship.
We discover that he was given a chance to save the human race, as the lead alien told Tom to tell his people to surrender in exchange for some kind of asylum/permanent imprisonment. He turned the offer down.
Back on earth, during his absence, it was clear that Hal took has taken on more responsibility, while questions still surround Ben and his physical abilities/mental state.