The Truth Behind the Aliens: The film's major twist is the confirmation that Brian was never abducted by aliens. The "missing time" and the "aliens" were his brain's way of blocking out the memory of being raped by the Little League coach. The "white light" was likely the light of the garage or bedroom where the abuse occurred.
Neil's Realization: Neil, who always remembered the events but framed them as a consensual romance, is forced to confront the reality that the coach did not love him. This culminates in New York when he is raped by a stranger, mirroring the powerlessness he actually felt as a child. He returns home not as a conquering hero, but as a broken boy.
The Reunion: In the final scene, Neil tells Brian the truth. Brian breaks down, finally remembering. Neil holds him, and for the first time, drops his cool facade to share in the grief, acknowledging that they cannot "magically disappear" but must live with what happened.