In the lab, Megan isn't happy to hear that there's DNA and fingernail polish that implicates Tommy as Skylar's murderer, and at the precinct, Tommy's boss, Chief Angela Martin (played by the fantastic Lorraine Toussaint) is also displeased. She tells him not to leave and warns Adam to get the case resolved as soon as possible. Adam and Tommy talk afterward, with Tommy suggesting they check out the bar's surveillance tapes. When Adam and Megan do so, they see Tommy leading Skylar from the bar. The lip-reader with them claims that he said "You're going to regret this."
A phone call from Ethan brings the two of them back to the lab, where Ethan shows them the recovered murder weapon - a man's belt - and that epithelials found on it registered another DNA match to Tommy. This is enough to get everyone's favorite detective formally arrested, while Adam and Megan look on, with Megan visibly upset.
Adam and Megan confer with Tommy again once he's in custody and ask him to explain the forensic evidence, but of course he can't. Megan further tells him that his blood work didn't show any drugs in his system. This makes Tommy finally flip out, and he angrily insists that he isn't a murderer. But how can they possibly prove it?
Megan returns to her office to find Chief Martin there, and Kate informs her that Martin wants updates on Tommy's case. "Detective Sullivan may not be the man you think he is," Martin tells her, going on to say that after they left the club, Tommy and Skylar apparently went to a nightclub where Tommy got into an unprovoked fight with the bouncer.
Furthermore, the case has prompted the NYPD to unseal Tommy's records there, and the reason why he left New York involves beating a suspect. Martin wants Megan off the case, and Kate informs her that she's agreed to the request. Megan makes her displeasure known, while Adam begins to wonder if his partner really did crack.
At home, Megan's mother suggests that her emotions are clouding her judgment, but Lacey encourages her mother not to give up on Tommy. Smart kid, that Lacey Fleming. Unable to sleep that night, Megan places a late-night call to Adam, wanting him to meet her at the nightclub where his partner allegedly fought the bouncer. "I think I can prove Tommy's innocence," she tells him.
The two of them arrive at the nightclub and question the bouncer. Megan wants to know all the details of the fight, including the specific location where it took place. She finds a bloodstain on the carpet there and immediately removes a sample - over the bouncer's objection - in order to see who the blood belongs to and what's in it. Since it was spilled ten hours earlier and hasn't had a chance to metabolize, it proves that Tommy was indeed drugged, as he'd suggested. There's Zolpidem in his system, which explains all of his symptoms.
Adam and Megan are encouraged by the test results, but Kate and Martin remain skeptical, particularly Martin, who seems like she'd rather see Tommy fend for himself. "That woman has an agenda," Megan tells Kate afterward, revealing her past with Tommy to her boss, who reiterates that she can't be on the case.
Megan's response is to bail Tommy out of jail herself, finding the two million dollars to do so, by putting pretty much everything she has up as collateral. She's also convinced Kate is going to fire her. "I don't want you to put everything on the line like this," Tommy tells her. Megan's only response is that she wants to know what really happened in New York. Tommy finally reveals that his sister died in a hit and run accident, and he lost control with the guy that killed her. That's the suspect that he beat up.