Holmes' father offers to get Holmes and Watson back in the good graces of the NYPD. Holmes doubts his father's sincerity, wondering what his father will eventually want in return. "There's always a cost," he tells Watson when he puts the offer to her. But eventually Holmes decides he'd be happier if he could work with the NYPD again and that it might be worth risking eventually owing his father.
Watson is harder to convince. She does some digging and notes that Morland Holmes' way of getting what he wants is not always, shall we say, above board. Questionable at best, possibly illegal at times. Still, she's willing to go along with what Holmes wants.
Part of their desire to go back to working with the NYPD is their current case as consultants with the FBI is far too restrictive. Their FBI handler is a helicopter parent and Holmes and Watson must revert to sneaking in order to get the info they need to solve the case. Note the parallel, though: Holmes and Watson do something illegal in order to get what they want, all the while claiming it's for the greater good. Just as Holmes Sr. claims he's clearing his son's path for the good of his son.
The case itself is moderately interesting: in a secure lab, two researchers, a test patient and a lab rat are murdered. The researchers were working on some government stuff, namely how to change people's minds through propaganda (aka brainwashing). Initial evidence points to a Chinese diplomat, but we all know the first suspect is seldom the last, and the episode goes through the usual rounds before landing in a somewhat interesting spot.
On the whole I found it better than the season premiere. I still don't feel the whatever I'm supposed to feel between John Noble and Jonny Lee Miller. Like there should be tension but there's kind of nothing. Which is maybe the point? But I feel like there should be something. The Watson-Holmes Sr. dynamic was only slightly better. Then again, when you start from a negative number, odds of improvement are greater. Right? So here's hoping, assuming Noble sticks around (he's in the credits but could always drop out again, I guess), it only gets better from here.