So, back on Earth, in the Antarctic circle, some people find a feckload of wreckage and, er, a frozen Borg drone.
They find another one, and move in full survey equipment. Couple of them examine Borg corpses and try to figure out what happened. Then one of the arms starts working. Lemme guess - this is wreckage from the Borg sphere from First Contact? They find nano-probes.
One of the scientists thinks they should allow the nanoprobes to continue regenerating the drones and see what happens. Oh yeah, that's going to end well. One of the drones comes back to life while a couple of the scientists are salvaging a transwarp coil. They race back... to find him being assimilated, and then they're jumped by the Brog.
A shuttle arrives to find out why they haven't heard from the survey team in three days and they find the base deserted. This is very The Thing.
Er, meanwhile, in an entirely different part of the galaxy, Archer explains that the Borg fecked off in the survey team's transport at warp. They set off in pursuit.
On the way, they receive a distress call from a frieghter and set off to help. It's under attack from the upgraded transport, which fires on Enterprise. Reed fires back, and the transport flees. Enterprsie retrieve two survivors from the freighter, who are being assimilated. Phlox doesn't know how to stop the nanoprobes...
Archer's found the story about First Contact in the database. Hahahahaha! Oh, crap, Phlox is being assimilated. The two survivors are now BORG and disappear into the maintenance shafts.
They detect the transport again (it's been even more upgraded) and set off in pursuit. Meanwhile, Reed finds the two Borg assimilating bits of Enterprise, and have to makes a retreat when they turn out to be immune to phase pistol fire. Archer solves the problem by spacing the Borg. Bye bye!
Now they just have to worry about what modifications the Borg made, and Phlox. Easy, stick him in a magnetic chamber and give him a EMP. Not that he's being assimilated all that fast.
Archer tells T'Pol he wants to try to take the crew of the transport alive so they can be taken home. T'Pol thinks it's too dangerous and they should destroy the transport.
Phlox comes up with a treatment involving dosing himself with radiation, and hands Archer a neurological toxin to use ih the treatment fails.
Enterprise finds the transport again and knocks it out of warp. However the Borg send a signal which activates the Borg circuitry which disables Enterprise. Archer: "They set us up!" The Bomb? The Borg give them a call and give the usual "Resistance is futile" speech.
Phlox goes into his radiation chamber and starts the zapping. Meanwhile, Archer and Reed beam onto the transport and wander around. How the hell did Reed make the phase pistols unadaptable to? Borg board Enterprise. Great, now you can disable a Borg by pulling wires. Reed and Archer transport back to Enterprise and blow the bombs they planted.
The boarding Borg disappear and the transport comes back online, forcing Enterprise to destroy it. Later, Archer and T'Pol visit Phlox, who is recovering and says at one point he felt he was part of a hive mind, and could tell the Borg were transmitting a message. After analysis, they find the numbers are coordinates to Earth, and were beamed to the Delta Quadrant, but they'll take some 200 years to get there. IE, sometime in the 24th century.