A probe from an unknown alien source unleashes a devastating assault on Earth, cutting a swath from Florida to Venezuela. Millions are killed, including Trip's younger sister, and Enterprise is called home. On the way back, the ship encounters a Suliban vessel that abducts Archer. Once again, Archer comes face to face with Silik and the mysterious humanoid figure. The figure informs him that the probe that attacked Earth was sent by the Xindi, a race that believes humans will destroy their homeworld in the future. They were given this information by individuals from the future who can communicate through time. The figure also tells Archer that the Xindi are working on a much more powerful weapon that they will use to destroy Earth. The humanoid figure believes that deploying such a weapon will contaminate the timeline.

Once Archer is returned to his ship and Enterprise reaches Earth, the crew is confronted with yet another obstacle — a Klingon bird-of-prey commanded by the vengeful Duras, who is determined to have his revenge on Archer and reclaim his honor. Luckily, a few Starfleet vessels are onhand to assist Enterprise in fending off the attack and the Klingons retreat. At Starfleet Headquarters, Archer tries to convince Admiral Forrest and Ambassador Soval that the threat the Xindi pose is very real. He even has a set of coordinates, given to him by the mysterious figure. The coordinates are inside the Delphic Expanse, an area that's something like the Bermuda Triangle of space. Soval and Forrest aren't convinced that Archer's information justifies a mission into this area. Luckily, the humanoid figure has also provided Archer with proof. Archer scans the remains of the Xindi probe with a quantum-dating device, which shows that some of the debris is from the future.

With this information, Starfleet gives Archer the go-ahead for a new mission to the Delphic Expanse. Enterprise is fitted with new weapons and equipment and assigned some military personnel. Meanwhile, the Vulcan High Command informs T'Pol that they do not want to her to go on the mission. — if she decides to remain onboard Enterprise, she will lose her commission.

Enterprise sets off, planning for a stop on Vulcan along the way to drop off T'Pol. First, however, they must deal once again with Duras, who attacks once again. The crew manages to fend him off using the newly-upgraded weapons. Meanwhile, T'Pol has come to a decision — she wants to remain on Enterprise. She has resigned from the High Command. With that settled, Archer sets a course for the Delphic Expanse.

As they approach the Expanse, Duras attacks once again — and this time, he has two other birds-of-prey to assist him. Though two of the Klingon ships turn back as they get close to the Expanse, Duras presses on. Through some clever maneuvering, Archer manages to avoid the Klingon ship and eventually destroys it. With no other obstacles in their way, the crew of the Enterprise bravely heads for the Expanse ... and the unknown.