When Bell gets to the brownstone, Holmes is behind a microscope, and Watson tells Bell they think someone's trying to frame him. Holmes reveals a gun, which he stole from Bell's home. When he went to the bathroom, there was the smell of a recently fired gun, which was in the vent in the bathroom. Holmes has verified (through home ballistics tests) that it's the same gun that killed Bradshaw.
Holmes Watson, and Bell have gone to the police station. Gregson agrees with Holmes that this was the gun that killed Bradshaw. Holmes's claim is that he found it in a dumpster. But there were no fingerprints, so Bell is officially still a suspect. On their way out, Holmes and Bell talk about why Bell is bad at lying, but Holmes is good at it. Holmes doesn't think Bell did it, because he's not an idiot. And the reason Holmes lied is that he doesn't want Internal Affairs around the place. He'd like to nose around Bell's place to look for clues, and Bell claims nobody but him has a key. He gives his key to Holmes. Then he looks thoughtful.
Andre comes to the police station to talk to Bell. Andre cheerfully points out he's not allowed to talk about criminal activity, and Bell brings him up to speed with the events of the episode so far. And the distinctive boot prints that point to Bell could also have been made by the boots in the box of clothes Bell gave Andre when he got out of prison. He could even have copied his house key when he stayed at Bell's place. Andre is outraged. Things have been strained between them ever since Bell became a cop. Bell complains that Andre was in jail because he wouldn't roll on his friends. Andre leaves without denying being involved. Then he punches Bell in the face, and Bell has to stop everyone from arresting him. The middle of the police station is not really the place to punch your cop brother.
Holmes is frustrated at the lack of evidence in Bell's apartment. He asks Watson, "Can you think of any reason that Bell would have a lingerie catalog on which your head has superimposed on almost all of the models? He hasn't. But can you think of any reason he would?" That's fun. Holmes is still frustrated that Watson won't learn self-defense. She tells him she's not his apprentice; she's his sober companion. But Holmes tells her she isn't! Holmes learned that she isn't when he called his father last week. Which is good because that's what everyone assumed. He's been acting very sober lately to show her that if she wants to leave, she could, "But the most curious thing happened. You stayed." He feels she was staying for herself. He asks her to consider a proposal: "Stay on permanently. Not as my sober companion. As my companion." He wants to teach her, and she'll receive a stipend. He has "certain funds set aside." She's also relieved of any confidentiality requirements about his sobriety. He encourages her to discuss this decision with others. He wants her to be a partner. Jonny Lee Miller's really good in this scene -- he's radiating. He begins to leave, and then he says "I am better with you, Watson. I am sharper. More focused. Difficult to say why, exactly. Perhaps in time I'll solve that as well." Great scene.