They simply have gotten used to each other's company; late nights working on cases and eating Chinese takeaway that ends with them falling asleep together either on the couch in her office or Booth's apartment, waking up with Booth spooned protectively behind her, encasing her between him and the couch, in-between case trips to the diner and during-case car rides had led them to this.
They still have their own, separate apartments for when they're needed, but most of their time is spent at the hidden, third, shared apartment, and bought under fake names with cash. She doesn't try to look too deep into how well they've hidden this small, one bedroom apartment with its kitchen/living room and a wonderful view of the office block next door, because looking into it means admitting there iis/i something here to hide. And really, there isn't. It's just two people sleeping in the same bed.
For comfort.
Luckily, however, before she can begin to panic, wonder if this apartment is a bad idea, if they should just go back to being partners who don't sleep in the same bed, Booth enters, stumbling, scratching idly at a bandage on his cheek from an encounter with a knife-wielding perp and the paperwork and interviewing that comes with knife-wielding perps. The FBI agent drops down onto the bed, wriggling out of his jacket and curling an arm around the Anthropologist and tugging her down, her back to his chest and she just... forgets.
She forgets about the panic, the 'should they, shouldn't they?', what they're trying to hide with the fake names and just relaxes back into him with a hum, eyes sliding shut as his face buries against the back of her neck.
"G'Night, Bones."
"Goodnight, Booth."
And it is, a good night.