Captain Archer and his crew discover that Dr. Arik Soong and his army of superhumans, the Augments, are bent on "awakening" thousands of genetically-altered embryos. That mission would render humanity extinct, as the Augments would take over mankind. Trying to find where Soong has taken the bird-of-prey which the Augments commandeered, Archer takes Enterprise to Trialas, where the Augments were "raised" years ago by Soong. There, Archer and Trip uncover Soong's plan, and realize that the embryos are on a medical research facility — which also stockpiles highly virulent diseases for research — called Cold Station 12. Soong is clearly making plans to incubate the embryos to be "born." While looking through the settlement where Soong raised the Augments — but left them a decade ago after being captured — the crew also finds Smike, a less-than-perfect Augment who has been left behind.
Certain that Smike can help him further unfurl Soong's plan, Archer ingratiates himself and eventually convinces him to join Enterprise's mission in stopping the Augments. As Enterprise heads to Cold Station 12, Soong and the Augments have indeed arrived, taking C-12 workers hostage and furiously trying to procure the embryos which are currently locked away. Soong and the Augments' self-proclaimed leader Malik bear down on the facility's medical director, Dr. Jeremy Lucas, a Denobulan and good friend of Dr. Phlox. At first, Lucas insists that he doesn't have the access code to free the embryos from their stasis chamber, but the Augments — with their superior abilities — soon learn otherwise, and threaten Lucas' life if he doesn't divulge the information they need.
Soon after, Enterprise comes near Cold Station, but Soong pledges to kill Lucas if the ship doesn't turn around. Though Archer initially accedes to Soong's command, he has another plan in mind. Mayweather then arranges to transport Archer, Reed, Trip, Phlox, Smike and MACOs onto Cold Station to thwart Soong's efforts. But shortly after they arrive on Cold Station, they are quickly overcome by the far-stronger Augments, who are completely impermeable to attacks of any kind. Soon brought to Soong — and reunited with his nemesis once again — Archer promises to prevail. And, in fact, when T'Pol hails the Station, Archer — though held captive — orders her to proceed with launching a destruct code, that Starfleet has given them, which will decimate Cold Station 12.
Though T'Pol carries out the order, the Augments are able to block the code. T'Pol then scurries to find other means to destroy Cold Station 12. Yet, as she does, Augments still in the commandeered bird-of-prey block Enterprise's every move.
Then, as Malik and other Augments realize Lucas' connection to Phlox, they threaten to kill the Enterprise doctor with a deadly pathogen on board the Station if Lucas won't give up the access code to release the embryos. Fearing for his friend's life, Lucas discloses the information they need. Soong is awestruck as he is reunited with the thousands of embryos.
Afterward, as Malik leads Archer and the others to a containment cell, he tells them that Soong and the Augments will be leaving shortly with the embryos. When they do, Malik says that they will also release a pathogen that will kill those left on Cold Station 12. And as his bravado reaches a fever pitch, Malik even kills Smike to prove his superiority. Helplessly, T'Pol and the others aboard Enterprise watch as the Augments' bird-of-prey looms nearby and Soong, Malik and the Augments — via a medical shuttle from C-12 — go aboard it with their released embryos in tow.
Left behind on C-12, Archer and the others now must determine a way off the station — or somehow stop the deadly pathogen's release — before they succumb to its fatal effects.