Mystery first - there isn't much of one. We're not really given anything to suggest who the kidnapper(s) is. As usual these days on "Monk," the only real clue is the lack of suspects and the almsot certain knowledge that the writers aren't going to throw a total stranger at us.
Non-Monk regulars: Disher gets a little more personality and you'd think that he'd try something (and overreact at trying something) to come across as more professional. Stottlemeyer doesn't have much to do. Natalie is adequate and gets a few moments as a "mother"-type without beating us over the head with it.
As with previous Monk season finales (and even half-season finales), this is realyl a Monk-centric episode. Tony Shalhoub rises to the challenge and the writers for the most part avoid going too overboard with the Monkisms. Only the locker room scene seems to go on a bit too long.
The real "acting" here is from Preston and Trevor Shores, and the chemistry between them and Tony Shalhoub. They haven't appeared in anything else, but it'd be a pity if they don't. The chemistry between child-actors and the parent-figures they're appearing with is desperately needed - ask Traylor Howard, who fails to bond at all with the Falconer twins in her recent Son of the Mask. (In fairness, neither does Jaime Kennedy.) Obviously Shalhoub is comfortable with them and vice versa, and it's critical for this episode to work. It helps that the kids, despite their youth, are good actors as well and bring a lot of talent to the scenes with the chessboard, cleaning the house, wrestling outside with Shalhoub, etc.
I think the "here's how they did it" wrap-up proves one point I've asserted before. When they do it every episode, it detracts from the individual ones. The storybook wrap-up here would have been much more effective if we hadn't seen similar "unique" wrap-ups in the last six episodes.
So that brings us to the season as a whole. Unfortunately, it's hard to judge the "season" as a whole when they split it up into two parts so widely-divided. The first issue was Bitty Schram's abrupt departure and the writers and producers moving to cover for it by introducing Traylor Howard's Natalie. The episodes that focussed specifically on her ("Red Herring," "Cobra," "Election") tended to go a bit overboard - they didn't really show her as much different from her predecessor. I get the impression the character isn't as strong as Sharona (a bit of a whiner, IMO)...except in the episodes that seem to have been rewritten with Natalie and were originally intended for Schram. It's in the episodes that don't focus so strongly on Natalie that Howard gets a bit more chance to shine and work in some subtle differences to her predecessor.
Overall I'd say Howard acquitted herself pretty well - hopefully the writers have gotten over their desire to "feed" her to the audience and can let her settle back a bit to get into the role. There are a few instances whent he writers didn't handle it very well, but then they didn't have much time to adjust, either.
Stottlemeyer seemed to get a bit more depth with his concerns about where his career is going and his cutting loose in "Las Vegas." Disher is pretty much still the buffoon although "The Kid" might suggest a bit of a change for him. Hopefully they'll stick with it.
The mysteries were a bit of a mixed bag - James Brolin was really the only killer who seemed a worthy match for Monk. They managed to avoid the more embarassing parts of the first half of the season ("The Panic Room" with both Monk and Stottlemeyer). Monk matured a bit, overcoming the adversity of losing his trusted assistant and gaining a new one.
So overall, the third half-season was a bit of a mixed bag, but overall the cast and crew managed to weather the loss of Schram and move on.