[Demonskid]

um.. she and booth had a baby girl and some bad guy used the computer systems and stuff to frame Bones of murder so she took her dad's advice to go on the run. So she took her baby girl while booth was trying to get their car, and went on the run.

They didn't tell booth about their plan so he could stay in the FBI and try to get the dude framing Bones

but the final scene you see is Bones Driving off with her little girl in the back seat