- 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.
- Picking up from the cliffhanger Affliction (2005), Enterprise's engine is sabotaged and near overload. The Columbia sends Trip to reboot the reactor. Phlox rushes to cure Klingon plague before the forced sterilization of the colony. With Reed in the brig, Archer contacts Harris for answers to the Lieutenant's betrayal.—Meribor
- Captain Archer finds out the Klingon augments booby-trapped Enterprise. The ship cannot drop below warp five. The Columbia comes to help. Trip has an idea to reverse the Klingon modifications, but at this kind of speeds he cannot use the transporter. Reed is taken out of the brig for a dangerous plan. Meanwhile Antaak and Phlox find a cure that will neutralize the virus without turning the victim into an augment. They fear general K'Vagh will not accept it and decide to deceive him. On Enterprise captain Archer finds out Reed was contacted by a certain Harris. He wants to know more, putting Reed in another dilemma.—Arnoud Tiele (imdb@tiele.nl)
- The only hope to Enterprise is the support of Columbia and Trip. Travis synchronizes the flight of Enterprise with Columbia while Reed brings Trip on board in a risky operation. Then Trip cold starts the reactor and repairs the system while Columbia sustains a warp field with the Enterprise. Both ships travel together to the genetic research facility in the Qu'Vat colony. Dr. Antaak and Phlox discover a cure, but they do not tell the General K'Vagh that the process of creating augments will be interrupted. Meanwhile Harris contacts Archer to discuss Reed's situation. Archer reintegrates Reed to his position, but demands loyalty from him. When the Enterprise and Columbia arrives at Qu'Var, they are attacked by the ships of Admiral Krell who has received orders to destroy the colony.—Claudio Carvalho, Rio de Janeiro, Brazil
- With the ship unable to decrease speed below warp 5, and the warp core reaching dangerous levels, Columbia and Commander Tucker rendezvous to provide assistance. However the crew realize that the transporter cannot be used at warp, so the ships will need to maneuver in close proximity in order for Tucker to be transferred. Captain Archer releases Lieutenant Reed from the brig to perform the transfer (he had performed the transfers in simulations at warp 1) (Reed and Archer merge warp fields of the 2 ships and deploy a tether to help Tucker transfer over). Once on Enterprise, Tucker successfully performs a rapid non-standard cold boot on the warp engine, which purges the Klingon subroutines. Tucker then agrees to remain on-board temporarily to assist with repairs.
Meanwhile, physician Antaak (John Schuck) and a badly beaten Doctor Phlox update General K'Vagh (James Avery) on their progress. K'Vagh contacts Admiral Krell (Wayne Grace), who tells him that if a cure is not completed soon, the facility will be eradicated in order to contain the disease. Antaak tells Phlox to complete the cure for the plague, but detach the genome sequence of the augment, ensuring that anyone infected doesn't get the enhanced speed, strength, agility etc. K'Vagh doesn't know that his son Marab (who was captured on the Enterprise) is still alive.. He was told that he died in the attack to sabotage the Enterprise engines. K'Vagh is determined to save the other Klingon soldiers who were infected by the virus, as part of the experimentation. Phlox develops 4 cures, but needs to test them. Only one will work and the other 3 will kill their hosts. K'Vagh forces Phlox to test it on 4 Klingons including himself to get the results in an hours. An hour later it is confirmed that K'Vagh has the cure and Phlox races to save Antaak, who is now infected.
Back on Enterprise, Archer questions Reed about his recent actions, and is contacted by Harris (Eric Pierpoint) from Section 31, a secretive agency within Starfleet. Harris reveals that Phlox is on an important mission and little else (and tells Archer to stay out of the mission as Starfleet needs a stable Klingon empire), but Reed reveals his location as Qu'Vat (When Archer tells Reed that he doesn't trust Harris and Reed has to chose where his loyalties lie); Harris contacts Krell, to inform him that Enterprise is on the way, and Krell reveals that he used Harris (he says he will destroy the Enterprise). Enterprise arrives at the colony, and Archer beams down to the base with Marab (Terrell Tilford) (The captured Klingon Augment) to confront the Klingons and Phlox. K'Vagh is surprised to see Marab alive, and infuriated when Phlox reveals that he is working on a cure for the virus and not perfecting the augments.
Krell's Klingon battle-cruiser and two Birds of Prey arrive in orbit and Krell orders the ships to destroy the colony. Enterprise attempts to intervene (Archer tells Krell that the cure is ready, but Krell wont listen) but is engaged by the Birds of Prey. Columbia arrives and joins combat with the two Birds of Prey, while Enterprise impedes the battle-cruiser by putting the ship in the path of its firing line on the colony. Meanwhile, Phlox infects a voluntarily restrained Archer, as he needs human antibodies for replicating the cure quickly. Antaak then transports a canister of the virus onto the battle-cruiser which infects the crew, including Krell. Needing the cure from Phlox, Krell stands down the attack and the Klingon High Council soon agrees to distribute the cure throughout the Empire. Antaak survives
Harris contacts Reed, thanking him and confirming that the plan proceeded as per Section 31's projections, stabilizing the leadership of the Klingon Empire while scaring it off from augment experimentation.
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