After receiving a warning about a radioactive storm approaching Enterprise, the crew is forced to take shelter in the ship's catwalk.

Enterprise discovers a pod with the body of a human that seems to be wanted by both Sulibans and Tholians.

At Dr. Phlox's request, Enterprise attempts to retrieve 3 Denobulan scientists from the planet Xantoras, where the Goverment has ordered all off-worlders to evacuate within 3 days. Tucker, Reed, and Mayweather navigate a series of labyrinthine underground caves in search of the scientists. Meanwhile, Enterprise lends assistance to a damaged ship fleeing the planet. Doctor Phlox faces an ethical dilemma when one of the refugees of the ship refuses life-saving treatment. The patient, an Antaran, holds a grudge against Phlox stemming from a war between their races that ended 300 years ago and would rather die than be treated by a Denobulan. Phlox defies Archer's direct order to force treatment because it goes against the Deobulan code to yield to "the will of the patient."

After exploring an uninhabited planet, Captain Archer is taken prisoner by a Tellarite bounty hunter who was hired by the Klingons to return Archer to Qo'noS.

Enterprise answers a distress signal from a stranded Vulcan ship, only when arriving they find the ship completely desolate, wrecked - and filled with Vulcan zombies.

While in command of Enterprise because the entire crew is in a coma, Dr. Phlox starts hearing some strange sounds.

Captain Archer has been returned to Enterprise by the Xindi council awaiting a hearing. But after a heavy attack by the Reptilians, Enterprise is stranded without a functional warp drive. They meet another ship in trouble because of space anomalies. The ship's captain isn't willing to trade in their warp coil and Archer must make a tough decision. Meanwhile T'Pol is having some strange sensations and can't control her emotions.

While the Reptilians force Hoshi to decipher a launch code, the Primates, Arboreals and Archer think of a way to stop the Xindi weapon.

Archer takes Degra's ship to try to prevent Earth from being destroyed and gets some unexpected help. Enterprise tries to destroy Sphere 41, but the Sphere Builders know about the plan.

Dr. Emory Erickson comes aboard to supposedly conduct tests for subquantum transportation. However, he seems to have a different agenda.

While Enterprise tries to bring Trip on board to reverse the malicious Klingon modifications, Phlox and Antaak find a cure for the virus that will not please General K'Vagh.

While attending a conference on a proposed interplanetary alliance, Trip and T'Pol find out from a dying woman that they have a baby. Investigation shows the woman was a member of the xenophobic organization Terra Prime.

Paxton threatens to destroy Starfleet Headquarters if all aliens don't leave Earth. Enterprise must shut down the verteron array on Mars, but it is extremely well defended.

In 2370, Commander William T. Riker is trying to clear his mind and relives the last mission of the first Enterprise on the holodeck.