The first witness was a friend of Joe Newell, the pilot. He also knew one of the passengers: Walter Devlin. He'd never met Hank Gerard (the murder victim), and Ellie Wilson, although he knows they worked together. Joe, he says, didn't have a temper and would be unlikely to bludgeon a passenger to death while he was supposed to be flying the plane. Also, Joe was ex-military. He offers up the information that there was a security camera in the parking lot that might show the passengers arriving. He insists that Joe didn't do it.
Continuing the subplot, Watson says she got an email from Holmes's father with a dinner appointment at a specific time and place. Holmes says his father doesn't care about him or her, and that he's not coming tonight. His father is a pathological maker and breaker of promises. This is interrupted by Bell, who says there's news. So Holmes, Watson, and Bell all have to traipse into Gregson's office.
Bell tells Gregson that the three lawyers on the plane were going to Martha's Vineyard to work on a suit against Carmonto Foods, which is exactly the kind of giant evil conglomerate it sounds like. They make a sugar substitute that causes cancer. Allegedly. The three lawyers disagreed about how to proceed and Hank had a loud argument with Walter Devlin. Holmes wonders why Walter would bring a giant wrench on the flight.
The plot can now proceed, because they finally have the flight recorder. The four of them listen to the sound of Walter Devlin yelling at Hank and also Ellie: "You can't protect Hank, Ellie. Not from me!" There's also the sound of a struggle and a plane out of control.. Holmes looks at the pictures of dead people on the beach. There are screams on the recording. Then Holmes says Walter's argument with Hank was one-sided; Hank never said a word. They had loud arguments all the time, but this time Hank never got a word in. And they have everything that was on the plane, but no wrench. Also, the pilot said "three souls aboard" when he was radioing for help. So Holmes's theory is that Hank Gerard was not in the cabin at all. He wasn't killed in the plane! The killer bludgeoned Hank Gerard, then hid the body in the cargo hold. Walter Devlin was on the phone during the conversation until Ellie dragged him to the back of the plane. And that shifted the weight in the plane, which made the unsecured body slide around in the cargo hold, thus causing the crash!
Conveniently enough, they have also recovered Gerard's cellphone, although they think it's broken. Holmes grabs Bell's phone and swaps out the SIM card. There is, in fact, a voicemail form Walter Devlin! So neither of the passengers did it, and the pilot would have known better than to let the body slide around in the cargo hold. So there's a living murderer somewhere! Which I think we all assumed from the beginning of the episode, but I guess we have to let the characters catch up with us once in a while. Holmes wonders why the body was stuck in the cargo hold. It would be found it landed, right? Watson asks if he's scared of flying. She thinks he's been acting weird, because he got distracted by sand earlier. He's acting exactly as squirrelly as always, and Watson should know by this point to stay out of his way. She really has no faith in him at all. Holmes points out she's a disgraced ex-surgeon, not a disgraced ex-psychiatrist. Burn! She asks how Holmes got from London to New York, because she's now convinced that he's afraid of flying.