Ianto was in the military/UNIT before being lent/given/transferred to Torchwood London. When that fell, he altered his records to show that he had only worked as an underling in London, instead of as something kick-ass. He is tired of killing and stuff like that, so he tries to hide himself by working as a tea boy in Torchwood Three.
So when somebody tracks him down and wants him back, he doesn't know what to do. Jack sees somebody in the military/Unit talking to Ianto and want to know what they talked about, but Ianto doesn't tell him. He does something searching and finds out about Ianto's past.
That is as far as I got before the bunny scampered off. I want there to be a nice or angsty ending, and the pairing to be Jack/Ianto.
Hope somebody writes this :)