Capt.Jean-Luc Picard inexplicably finds his mind jumping between the present (stardate 47988) and the past just prior to the USS Enterprise-D's first mission six years earlier at Farpoint Station and over twenty-five years into the future, where an aged Picard has retired to the family vineyard in Labarre, France. These jumps occur without warning, and the resulting discontinuity in Picard's behavior frequently leaves him and those around him confused.
In the future, he gains passage on the USS Pasteur, which is under the command of his now ex-wife, Dr. Beverly Picard, whom he convinces to find the anomaly.
In the past, despite having the Enterprise's mission to Farpoint Station cancelled by Starfleet to investigate the anomaly, Picard insists on continuing, believing the impending encounter with Q to be more important. After reaching the place where he had first encountered the Q in the form of a net near Farpoint Station and finding nothing there, Picard enters his ready room, only to find himself once again in Q's courtroom. Q reveals that the trial started seven years ago never concluded, and the current situation is humanity's last chance to prove themselves to the Q Continuum, but secretly reveals that he himself is the cause of Picard's time jumping. Q challenges Picard to solve the mystery of the anomaly, cryptically stating that Picard will destroy humanity.
As Jean-Luc Picard arrives at the anomaly in all three time periods, he discovers that the anomaly is much larger in the past, but does not exist at all in the future. As the past and present Enterprises scan the anomaly with tachyon beams, the USS Pasteur is attacked by Klingon ships, but the crew is saved due to the timely arrival of the future Enterprise under the command of Admiral William Riker. He fires on several of the attacking Klingon warships, which causes them to flee the neutral zone. It is revealed that Riker and Worf are in a feud over the late Enterprise counselor Deanna Troi, with whom both had a serious relationship and who had died years earlier. Q once again appears to Picard and takes him to billions of years in the past on Earth, where the anomaly, growing larger as it moves backwards in time, has taken over the whole of the Alpha Quadrant and has prevented the formation of life on Earth. When Picard returns to the future, he discovers the anomaly has appeared, created as a result of his orders, and the tachyon pulses from the three eras are sustaining it. Data and Geordi determine that they can stop the anomaly by having all three Enterprises fly into the centre of it and create static warp shells. Picard relays the orders to each Enterprise. Each ship suffers warp core breaches, with Q telling the future Picard that "all good things must come to an end" just before the future Enterprise explodes.
Picard finds himself facing Q in the courtroom as before. Q congratulates Picard for being able to think in multiple timelines simultaneously to solve the puzzle, which is proof that humanity can still evolve, much to the surprise of the Q Continuum. Q admits to helping Picard to solve it with the time jumping since he was the one that put them in this situation, and then goes on to explain that the anomaly never actually existed and that his past and present have been restored. He then withdraws from the courtroom and bids farewell to Picard by saying "See you ... out there". Picard then returns to the Enterprise of the present and no longer jumping through time.
As the senior staff plays their regular poker game, they reflect on the future the captain told them, to prevent them from drifting apart. For the first time ever, Picard decides to join the game, expressing regret he had not done so before, saying "...and the sky's the limit," suggesting more adventures lay ahead for the crew.
The idea of what the series finale should be about had been a matter of discussion in the writers' room for a year or two prior to the finale being written. The writers knew early on that they wanted to do a Q show, a "bookend" to the entire series. An early draft of the script for the episode included a section with Captain Picard as Locutus of Borg, but that was cut on the insistence of Michael Piller, the show's head writer and one of its executive producers, who thought the show worked best with fewer timelines to jump between. Also cut from the script was a segment where the crew had to steal the Enterprise from a Starfleet museum (similar to events in the movie Star Trek III: The Search for Spock). The final scene, in which the crew play a hand of poker together, was the last scene shot for the show.
A behind-the-scenes retrospective documentary called Journey's End: The Saga of Star Trek: The Next Generation, hosted by Jonathan Frakes, was filmed at the same time as the finale was being produced.
The episode ranked fifth in Entertainment Weekly's list of top 10 Star Trek: The Next Generation episodes.USA Today called the two-part finale a "picture-perfect" ending to the series, giving it 3 1/2 stars out of 4.The A.V. Club gave both parts of the two-hour finale an 'A' rating.