Previously blah blah space ninjas kicking Klingon arse blah Brent Spiner blah etc blah
Archer works feverishly to prevent the pathogen release, and ends up isolating the room everyone else is in, but only has a minute to go before the release. No problem, get Enterprise to beam him out. Oh, wait, title sequence first.
They can't transport Archer out because of interferenece, so they blow a nearby hatch, shooting Archer into space then transporting him from there.
Brent and his Augments nip over into Klingon space, where Malik breaks the news he killed Archer. Brent is not happy.
Archer recovered from decompression in sick bay while they discuss how to follow the Augments without the Klingons coming and kicking their arses.
The Augments are heading for "The Briar Patch", a hostile region of space, to hide out. The Briar Patch was, of course, featured in Star Trek: Insurrection. Then there's a discussion about Khan and the Botany Bay.
Trip modifies the Warp signature to look like a Klingon warp signature, and they head off after the Augment ship.
Brent tells Malik off for disobeying him. Brents also fiddling with the genome of the embyros to remove some defects re agression, which annoys Malik a bit. Then they detect Enterprise coming up behind them and a firefight ensues.
The BOP drops out of warp and drops the Denobulan pilot out in a shuttle. This forces Enterprise to stop to mount a rescue mission while the BOP continues on. Malik suggests using one of the pathogens against a Klingon planet, provoking a war which will keep Star Fleet busy for years. Brent tells him to STFU and go back to the bridge.
Enterprise finishes rescuing the Denobulan who shall not be named, and they set about looking for the BOP again. T'Pol engages Trip in conversation and asks why he's avoiding her. Then they have a conversation about T'Pol's recent marriage until they locate the BOP again.
Malik tells his girlfriend he's decided to take over from Brent. They confront Brent and decide to lock him in his quarters.
Enterprise detects a Klingon ship incoming, and... hang on, in Star Trek: the Undiscovered Country, Uhura says they can't use the universal translator when pretending to be a Klingon ship because the Klingons would recognise it. They have a better Universal Translator in Enterprise than they do in the movies set in Kirk's time?! WTF?! Or is it just Klingons in Archer's time are dumber? Anyway, Archer successfully bluffs his way through the conversation by claiming the Chancellor is on board.
Malik's girlfriend helps Brent escape the ship in an escape pod which
Meanwhile, Malik knows that his girlfiend helped Brent escape, and they have a fight. Malik wins: FATALITY!
Another Klingon vessel, a battlecruiser, is coming in to intercept Enterprise, adn they're not taken in by the fake warp signature. They unsuccessfully try to negotiate, then drop out of warp, and damage one of the Klingon ship's nacelles with their grappler.
The Augment ship nears their target planet, with Enterprise in pursuit. Enterprise reaches the system after they've already fired, and Reed torpedoes their torpedo. With Brent's help, they disable the BOP, but Malik starts an engine overload. Brent tries to talk him down, but Malik won't listen, and the BOP goes boom.
However Malik has transported over to Enterprise, and attacks Brent before Archer shoots him.
Much, much later, Brent is returned to his cell, where he ruminates that trying to improve the human race is pointless, and working on a artificial life form might be more productive "but it may take a generation or two". Teh End.