Neither Beverly's tests nor Worf's security scans show any indication that Picard physically left the ship. The investigation is then put on hold by news that several Romulan Warbirds are headed for the Neutral Zone, toward a spatial anomaly in the Devron system. Picard is transported back to the future, where he remembers bits and pieces of what just transpired, then tries to explain this to Geordi, who is unconvinced, blaming it on Picard's disease. Geordi is worried enough to take Picard to Cambridge, where Data is a professor. Data decides to explore the possibilities, but Picard is transported back to the past, arriving at the point of his initial arrival on the Enterprise. Among the crew, he sees a group of scraggly humans laughing at him, a sight he has already encountered twice in the future. This is enough for him to suddenly declare a Red Alert.

Since he has foreknowledge of future events, Picard decides not to tell this crew what is happening. He senses a connection when he is told that several vessels are moving toward an anomaly in the Devron system. Starfleet cancels the ship's mission to Farpoint Station, but Picard insists they go there anyway and refuses to explain his decision to the confused crew. Soon afterward, he finds himself back in the present in Beverly's office. She scans Picard, and learns that he has accumulated over two days worth of memories in just a few minutes — real confirmation to what Picard has been saying.

Still in the present, Picard and the crew ponder the significance of the anomaly, which occurred in both the present and the past. Exhausted, Picard lies down in his Ready Room, then finds himself in the future. He insists in going to the Neutral Zone to find the anomaly, causing Geordi to worry about Picard's sanity. Still, he, Data, and Picard ask Riker, who is now an admiral, for help. However, since the Klingons, who have taken over the Romulan Empire, closed their borders to Federation starships, and now control the area, Riker is unwilling to let them proceed. Data proposes they instead travel on a medical ship, and they wind up on a vessel commanded by Beverly, now Picard's ex-wife. Geordi suggests that Worf, who is a governor in the Klingon Empire, might help them enter the territory. Picard then returns to the past, still on course for Farpoint. Suddenly, he finds himself face-to-face with Q, in the courtroom where they first met seven years ago.

Q offers to answer ten "yes" or "no" questions. Picard learns that his time shifting is connected to the "trail" Q put him through seven years earlier, that the spatial anomaly in the Neutral Zone is involved, and that a verdict has been rendered humanity will be destroyed. However, while Q is causing Picard to shift through time, it is Picard, not Q, who is responsible for the imminent destruction. Picard then wakes up in his Ready Room, in the present, and declares a Red Alert...

After his encounter with Q, Picard assembles the senior staff, and wonders if Q is actually giving him a chance to save humanity by showing him that the spatial anomaly also exists in the past. As they talk, the ship reaches the Neutral Zone, then Picard returns to the future, where Beverly's ship is also on the edge of the Neutral Zone. He convinces a reluctant Worf to accompany the group into Klingon territory, and then travels to the past, where he orders the crew into the Devron system. Finally, he returns to the present, where he is able to get Tomalak, the Romulan Commander on the other side of the border, to agree to entering the Neutral Zone together. Now heading for the anomaly in all three time periods, Picard learns that it exists in the present, and is larger in the past, but does not exist in the future.
Picard cannot understand why the anomaly is missing, and Beverly gives Data six hours to scan for the anomaly using an inverse tachyon pulse, then reminds Picard that this all might be a delusion. She leaves and Q reappears, again saying that it is Picard who destroys humanity. Picard then returns to the present, and suggests using the tachyon pulse to penetrate the anomaly. When Data begins sending the pulse, Geordi's eyes mysteriously start to rejuvenate. Data theorizes that this is because the anomaly is an eruption of "anti-time" — which has collided with normal time to create a rupture in space that is causing people to revert to an earlier stage of development. Picard then returns to the past, and suggests again that Data use a tachyon pulse to scan the anomaly. After this, he returns to the future, where Beverly's ship is attacked by Klingon forces.

The U.S.S. Enterprise, with Riker in command, appears and saves the medical ship, then brings the crew aboard just before the vessel explodes. Picard frantically insists that Riker continue the search. He then returns to the present, where Beverly tells him that the anomaly is affecting the entire crew. Picard orders Data to find a way to collapse the anomaly, at which point Q appears again. He takes Picard back to primordial Earth, where the anomaly fills the entire sky and a pond of amino acids is about to form the first protein. However, when these first building blocks of life fail to coalesce, Picard then realizes that his own actions somehow caused the anomaly, which then prevented the beginning of life on Earth.

In the past, Troi informs Picard that the anomaly is beginning to affect people there. Picard meets with Data and O'Brien, but they are unable to scan the anomaly enough to completely understand it. Returning to the present, Picard has Data change his scanning methods, which allows them to discover that their tachyon pulse is converging with two identical pulses at the center of the anomaly. Picard realizes that these scans must be from the other two Enterprises. He then finds himself back in the future, where he tries to convince his former crew that he is right. Luckily, Data sees the logic in what Picard is saying, and helps him explain that the anomaly could have formed in the future, where they are, then grow larger as it moved backward through time. Theorizing that the convergence of the three pulses ruptured the subspace barrier and caused the anti-time reaction, the group decides to return to the Devron system to see if the anomaly has begun to form.

Back in the Devron system, the crew detects a very small version of the anomaly. Data suggests shutting down the tachyon pulses, then Picard returns to the present and orders their pulse disengaged. The anomaly, however, remains unchanged. Picard then returns to the past, where he again has the pulse shut off. Again, the anomaly is unaffected. Back in the future, Data decides that their only option is to repair the rupture by taking the ship inside the anomaly, using the engines to create a static warp shell which would separate time from anti-time. This must, however, be done in all three time periods in order for the anomaly to collapse — which could quite possibly destroy all three ships. Picard returns to the past and gives the order, then repeats it in the present. Finally, the future Enterprise heads into the anomaly. All three ships reach the center and initiate the warp shells, and the anomaly begins to collapse. As it does, the past and present Enterprises are destroyed, then Q appears with Picard just as the future Enterprise is about to explode. Suddenly, Picard finds himself in the courtroom, facing Q again, who tells Picard he has succeeded in saving humanity. Picard is returned to the moment his adventure began, coming from the Turbolift in his bathrobe. He shares his experience with the crew, using what he has learned about the future to forge a new, closer relationship with his dearest friends.

Whoopi Goldberg was supposed to reprise her role as Guinan, but her film career kept her busy and so she was written out of the script.

After its initial release as a 2 hour season finale, this episode was edited for syndication into two hour long episodes with some scenes deleted. These include: An exchange between Picard and Tomalak - After Picard suggests one ship from each side enter the Neutral Zone, Tomalak asks whether the idea has been approved. When Picard tell him it has not, he responds, "I like it already." An important exchange on the Pasteur between Picard and Q, in the guise of an old man. A scene on the "future" Enterprise - While the crew are discussing their situation, Picard is seen wandering a corridor, stopping to ask a low-ranking crewman the way to Ten Forward. Also, a short recap "Last Time on Star Trek: The Next Generation" was added to the beginning of the second part, just like other two-part episodes from earlier in the series.