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.