He tied her up and brought her back to the farmhouse much to the dismay of Emma and Jacob. Jacob tried to convince Paul to get rid of her but he stated he was tired of being the third wheel and threatened to expose Jacob's secret if he didn't help him. Jacob sighed and helped take Megan down to the basement.
In the next episode Mad Love Emma demands that Megan be killed and Paul tells Jacob to do it and threatens him once again with his secret. But Paul tells Emma anyway which is the fact that Jacob has been lying and that he never killed anyone. Emma confronts Jacob later and forces him to go downstairs and kill Megan. No matter how hard he tries he can't do it. And eventually Megan convinces him to let her go. Megan runs out of the house but is eventually caught and stabbed (fleshwound) by Emma. Paul and Emma tie her up again and lock her in the basment. They tell Jacob they aren't giving up on him and he gets another chance to kill Megan.
Jacob continues to try to kill Megan in the events of The Siege but he cannot bring himself to do it. Towards the end of the episode Ryan Hardy finds Megan and she begs to be let go. Ryan says he cannot do that at this time and puts the tape over her mouth.
During the events of The Fall she is used as a barganing chip to keep the FBI and Ryan under control. This works until Emma escapes with Joey and the FBI storm the house. Megan is set free from her captors.