HRG said during the last episode of season 2, that he will work for the company in return for his family's safety yet when this season aired he's in jail. There can't be a time skip because Nathan's assassination follows straight after season 2. So why is he locked up?

Hiro cannot see himself in the future for if he were to remove himself from the present he can't exist in the timeline from that point onwards. However there is an explanation for Season 1 because the future Hiro that meets Peter in the train can return to that alternate future to meet himself in the loft.

I think that Bob told him to tell his family that, but that the plan was never that he'd be an agent again. It was only something to ensure that Claire wouldn't say anything.

Why did Noah leave a box full of top secret files in the middle of the room? And when he was "arrested" the Company would have taken care of that.
Hiro seems to be the boss for some time now, but the episode takes place right after Nathan's assasination.



This explenation doesn't convince me

All that Noah said is the deal was that he had to go back with them. No-one ever said anything about him bagging and tagging again. Bob was probably saving him for something, though. It doesn't matter now Angela's in charge, though. I wonder why Bob was above Angela in the Founders' food chain...

At the end of the second season, Claire was getting multiple boxes ready to expose The Company. She didn't have much time to put all of the boxes away...