With the nature of Tony's new mission, which spanned several months and was hidden to the rest of the team, it was necessary for the writers to use a framing device and create an excuse for Tony's memory, and the episode turned out fine. The scenes of Dr. Rachel and Tony at the hospital aren't particularly riveting, but Michael Weatherly surely acts well enough so that we know there is something very wrong.
Then, the mystery unfolds in between, as the writers slowly dole at pieces of information. As it turns out, the broad strokes of the plot weren't too complex, although there are a couple unanswered questions which probably will never get answered. Tony was tasked with finding Cade and found EJ to help him, but in the end, Cade was innocent and the real bad guys are Stratton and the Office of Naval Intelligence guy played by Philip Casnoff. Stratton framed Tony for an agent's murder, but everything is cleared up now. Yes, there are many questions about various characters' motivations and the plot was overly complex, but we get a general idea of what happened and the writers were never sticklers for plot details.
Since there wasn't any evidence to follow up on Stratton, NCIS will return back to normal next week and the week after that. Those who didn't the episode have nothing to be worried about, and those who did like the episode got a special treat.