Well, I thought about it for a long while and here's my conclusion. But first – one of the most popular theories, passed along by a future in-law and written about very well by Teflon at Molton Thought: Tony got whacked.
[Mr. Sulu, engage Spoiler Vision.]
In other words, maximum checkout. And Chase certainly set it up that way – besides the guy heading for the bathroom, Tony wound up living out a ton of Godfather parallels throughout the episode: the orange he tears into early on (a BIG harbinger of doom in the Godfather movies); the stray cat he picks up that annoys his capos (and that fixates on Chris Moltisanti’s picture at the Bing); the war with the New York families; even AJ’s decision to join the military.
Chase previously stated that the key to the finale was in the first episode, which featured Tony's brother-in-law Bobby musing that when you got whacked, you wouldn't even see it coming --just "nothing". Chase builds tension unbearably throughout the final moments of the show, as minute after minute drags by. The guy in the Members Only jacket goes into the bathroom (shades of "The Godfather"), Tony is momentarily distracted by Meadow entering the diner, and ---- NOTHING. Precisely as Bobby described it.
It’s a good theory, and it would be just like Chase to give so many people what they expected, but in an unexpected fashion that ensured that it kept the proper impact. However, I think there are other hints to support an alternate theory: Life goes on. (As above, highlight the empty to read.)
First off – Bobby himself didn’t die the way he described it. He got rather a good look at his two killers, absorbed a half-dozen shots at least, and finally toppled over into the train display. For that matter, Sil didn’t go out that way either. It was Phil who never saw it coming. Chase set up the payoff, and even alluded to it right before the final cut – and then never gave it.
Second, all through this episode, Chase does a great job of returning Tony to status quo. I thought it would be interesting for him to flip to the feds, and go into Witness Protection as James Finneran, his coma-induced alter-ego from last year; but honestly I had no idea how he was going to get out of the New York war going into the finale. It turns out that he doesn’t, really – he just gets a colossal reset. The distraction with the Arabs comes to nothing; he faces indictment, but as his lawyer says, “We knew this day would come”; he loses Melfi but starts an impromptu session with AJ’s Melfi-look-alike therapist – complaining once again about his mother even though she’s been dead for years; and as is usual, he’s able to cajole/bully his capo (this time, Paulie) into giving in to his wishes. Nothing changes. As AJ does not quote during the episode, “This is how the world ends; not with a bang, but with a whimper.”
It’s not just Tony, either. AJ, who shows alarming signs of adulthood, is lured away from any self discipline or responsibility and back into a cocoon of privilege , money, and screwing up; Janice is still manipulative and self-absorbed; Carmela is still bitterly competitive about Meadow (the scene with Meadow’s reformed party-girl friend is priceless – Carm is gleeful when she can remind her of her past, but the second she hears that the girl has cleaned up and is now in medical school, she coldly ignores her and leaves the room). And Tony’s Family, as Phil correctly observes, is in the end little more than a crew – Vito gone, Chris gone, Bobby and Sil soon to join them, and their “business” drying up or defecting to New York. Even as the big boss Tony commands nothing more than he started with in the pilot. He’s back to square one.
Finally, there’s the key scene, Tony visiting Uncle June. He goes unrecognized. Even when he brings up the shooting from the beginning of last season, Junior is nonplussed, and when told that he and Tony’s father used to run North Jersey, he remarks, “Oh, that sounds nice,” as if it had happened to someone else. And he can’t help Tony at Tony’s most noble – trying to make sure Bobby’s kids are taken care of.
When Tony leaves, it’s with the sickening certainty that he IS Uncle June. He even killed his own nephew the way Uncle June tried to kill him (twice, mind you). In the diner, with his family, he’s constantly looking over his shoulder. And even if he survives, how does it end? With him in a public nursing facility, abandoned, while his family pick over what’s left?
So those are the leading candidates. Others may occur to you, especially if you think I’m cracked.