The ending has the family in a boarded up house, having "the last supper," and talking about when their sons had their first big Fourth of July. Then comes the alien invasion of the house, leading up to the family being surrounded, and the elder son being shown a different reality, which leads to him being taken.
Cut to three months later. The family has moved into an apartment. The dad is talking to their lawyer over the phone about what happened. The mom (Keri Russell) goes to check on the younger son who has drawings of the aliens and the elder son in a pod.
Cut to flashbacks about him being sick.
The movie ends with the elder son calling his younger brother over the radio.