After being captured by Bristow's team on behalf of APO, a genuine black-ops CIA office, Gibson was shown hard evidence the Shed was a criminal organization.

The episode "Solo" strongly suggested Gibson, though she is no stranger to death, had herself never used deadly force up to that point (and continued to avoid doing so).

In the closing episodes of the series, Gibson found herself attracted to Grace even as she carried out an "off-book" investigation of the agent's activities.

In the series finale, Gibson was kidnapped and tortured by Julian Sark (with whom she had had a one-night stand while she was on an undercover mission for APO), and forced to help Arvin Sloane locate a cave he needed to find to achieve his endgame.

Following Grace's death and the massacre by Kelly Peyton of the twelve leaders of Prophet Five, Rachel realized she and her family were no longer in danger.