“The Augments” is episode six of season four of Star Trek: Enterprise.
In the previous episode, “Cold Station 12”, Malik had dropped the stasis fields on the station, meaning it will soon be flooded with pathogens. Captain Archer manages to isolate the control room, then has T’Pol blast the hatch where he is, so he can be transported when he’s blasted out into space and away from the interference.
Soong arrives on the bridge of the Bird of Prey and Malik tells him they’ve crossed into Klingon space. Enterprise is holding position; Soong comments that Archer isn’t foolish enough to follow. Malik tells Soong they won’t see Archer again; he’s dead. There was no option. Soong isn’t happy. He tells Malik to go to engineering to repair something. Malik says he isn’t an engineer. Soong says he’s a bright boy; he’ll figure it out.
The station has been evacuated and the captain seems okay and is being checked out in sickbay whilst he’s told the current situation. He asks if there’s anything they can do to stop from showing up on Klingon sensors. Trip suggests painting a Bird of Prey on the hull. Reed suggests faking a Klingon warp signature. Trip says it’s doable. The captain tells Phlox that Dr Lucas is heading back to the station to start cleaning up.
Soong wants the Bird of Prey to head for a region of supernova remnants he calls the Briar Patch once through Klingon space. The Klingons have never mapped it and there are signs of at least two habitable planets. It’s unlikely anyone will find them. Malik is unhappy they are hiding; Soong tells him the embryos need to mature in a safe environment. Malik doesn’t think a gas cloud will protect them from Starfleet. He mentions Botany Bay. The ship of Khan Noonien Singh. The ship, not the colony. Soong thinks it’s a myth. Even if not, it was lost. That’s Malik’s point. Khan was a great leader but made the mistake of running from his enemies, not confronting them.
Enterprise is following. They will detect as Klingon from a distance, but not if they are too close.
Soong is working in his lab when Malik joins him. Soong is getting the embryos ready to incubate. He’s also removing their aggressive and violent nature; a defect in the genome. Malik does not agree with that. Persis contacts Soong from the bridge; there’s a ship approaching at high warp. Enterprise. Persis informs Soong they have minimal aft weapons.
Archer opens a channel to the Bird of Prey; Soong thinks he sounds pretty confident for a dead man. Both ships open fire. Malik wants to engage; Soong says Enterprise outguns them three to one. Instead, he has the Denobulan pilot they captured put into a shuttle which is then dropped into a gas giant. Soong tells Archer that the pilot will be safe for 4-5 hours. Enough time to mount a rescue mission.
The Bird of Prey is being repaired from the damage Enterprise did. Malik tells Soong he took biogenic agents from Cold Station 12. They can be loaded into a torpedo. Not fire it at Enterprise; fire it at a Klingon colony. Once the Klingon High Council hears humans did it, they will declare war and keep Starfleet busy for years. Soong disagrees with this.
T’Pol and Trip end up making awkward conversation about her marriage. Trip says that, tough as it was to watch the ceremony, he’s proud of her for what she did. And it was probably for the best. A Vulcan and a human probably wouldn’t work out. Then they detect something and tell the captain they think they found the Bird of Prey.
Malik tells Persis he’s taking command. Everyone on the bridge is behind him; he needs to know where she stands. Malik has a plan to protect them from Starfleet and the Klingons but Soong won’t even listen. He’s altering the embryos’ genome, making them weak and docile like ordinary humans. Soong is found in his lab. He comments on how it needs four Augments just to confront him. Malik orders him confined to quarters.
Soong is concerned that the Augments’ behaviour will just make everyone else believe they are right about the Augments. Probably because they are. He’s now discovering the problems with them and just why they caused a world war. Captain Archer now has to stop Malik from causing an interstellar war.