Wesley accidentally releases nanites on the Enterprise. They then become self-aware and nearly destroy the ship before Data can establish communication with them. The Enterprise is also harboring a scientist who atagonizes the nanites out of fear that they will interfer with his research aboard the Enterprise. He nearly gets himself killed, but after Picard offers to bring that nanites to an unoccupied planet, every one goes on their merry way again. Wesley feels ashamed for his part on the near-disaster. Crusher has returned, and several crew members have been promoted since the end of the second season.
Ok, I had to get that out of the way first. I never hated the other doctor, but she was never Dr. Crusher, and I like the idea of the mother-son relationship being part of the show. I'm sure that has nothing to do with my having children myself, or that they're both boys. I'd apologize for the tangent, but actually, this episode is mostly about Wesley, the fact that he's growing up, and what that means for his relationship with his mother.
Every one has those mistakes that turn out to not only be really dumb, but really important. For instance, when I was young I accidentally broke a car windshield because I was throwing rocks up into the trees, trying to get a toy down. Yes, I was old enough to know better. I was also old enough to know that the broken windshield was a big deal. That was the day I learned what it really means to tell the truth even when you really, really don't want to. But even if you learn that lesson at a young age, sometimes older children (and adults) convince themselves that they can fix the problem on their own before they have to tell any one. It feels like it should erase the mistake, as much as a mistake can be erased.
The problem, then, can come when you can't fix the problem yourself. It's the big mistakes and the important mistakes that suffer the most from this. They're also the ones that you most wish that you could erase. Stupid reality. Stupid nanobots, eating the ship and becoming sentient.
Wait, take that back a step. It's totally awesome that they become sentient, and Wesley can almost take credit for that. If he'd invented sentient robots without the big mistake looming over his discovery, we'd have to hate him, but as it is, we see that he does have flaws that are't totally annoying. Must be why his mother keeps him around, eh?