After reconnecting with her through Second Reality six years after they broke up, Owen tried to recruit her for Torchwood Three. Unfortunately, they were tricked into having Bruydac control devices implanted in them. Megan was sent to retrieve the uranium cores that Guy Wildman failed to bring back.
When Jack Harkness realised that Megan was possessed by the same being as Guy had been, she threatened to smash two of the cores together to cause a small atomic explosion. Jack shot her in the head and killed her to prevent this. (PROSE: Another Life)