User blog comment:Jackalex13/Since when did Lucy started workin with da templars./@comment-4955322-20120326065527

In a nutshell, she got annoyed with the Assassins and William Miles for leaving her with the Templars for so many years and so just decided to join them instead, sometime before Assassins Creed 1. It's also why Juno's hologram forced Desmond to stab her. At least that's how I understand it.