For most of the franchise’s history Star Trek has used episodic storytelling. Especially in the Original Series and to a lesser extent, TNG, there were several stand-alone episodes where the character development did not carry over. But in the 90s, overarching stories were introduced, and Deep Space Nine used arcs in several of its seasons, especially with the Dominion War. By the time Enterprise aired, the writers experimented with a season-long arc. The second season finale sets up an attack on Earth by an alien probe where seven million people are killed. The crew spend season 3 of Enterprise tracking down the Xindi to prevent another attack.
In the beginning of “Twilight,” Captain Archer is woken up by a battle and rushes to the bridge in his pajamas, just in time to see the Xindi superweapon complete its mission and destroy Earth. He has been relieved from duty since developing anterograde amnesia thanks to a spatial anomaly. T’Pol is in command and receives a field commission of Captain. Once Earth is destroyed, Enterprise leads a convoy of survivors to settle on Ceti Alpha V—the same planet Khan is marooned on. For the next 12 years, Jonathan Archer wakes up under the impression that he still in command of Enterprise, and had just saved T’Pol from a spatial anomaly. Every day she has to tell him what has happened.
Doctor Phlox arrives with a bit of good news. After 12 years, he finally has a cure for Archer. The parasites that caused the amnesia have been very resistant to treatment. It doesn’t take long for Phlox to discover they exist outside of normal spacetime. They need to return to Enterprise, which has been patrolling the sector since the colony was established on Ceti Alpha V. Most of the crew has remained on board. After T’Pol resigned from Starfleet to care for Archer, Tucker and eventually Reed were made Captain. When Archer, T’Pol, and Phlox arrive on Enterprise, the crew hosts a reception for their former captain.
In Engineering, Phlox uses the energy from the Enterprise to target a small batch of parasites with antiprotons. It seems to be a success, and T’Pol notices that the scans from 12 years ago also has fewer parasites. Phlox deduces that if they eliminate Archer’s parasites in the present, then the infection never happens in the past. Perhaps that’s a key to saving Earth from the Xindi. But before they can start more treatments, the crew discover a small ship hiding in the edge of the system’s star. The Xindi hired someone to track Doctor Phlox and they know he visited Archer. It isn’t long before another attack is underway.
Now it is a race against time to cure Archer of his parasites. The Xindi continue their attack, destroying the bridge entirely and boarding Enterprise. When T’Pol and Archer return to Engineering they find the chamber damaged. The only other way to eliminate the parasites is to create a subspace implosion. So while the Xindi move systematically through Entreprise, shooting everyone they encounter, Archer uses the warp core to trigger a subspace implosion. At the last possible moment Enterprise is destroyed.
The next thing Archer knows, he wakes up in sickbay in the present timeline. He never contracted the parasites and only suffered a mild concussion instead. The past 12 years never happened, and Earth is safe, at least for now. The crew can continue on their mission to hunt for the Xindi superweapon.
To be perfectly honest, “Twilight” did not hold my attention very well. I sought it out for Boldly Going because it’s one of the highest rated episodes on IMDB. I had seen it before many years ago, when I bought a DVD collection of alternate reality episodes. I think because I haven’t seen much of Star Trek Enterprise, especially season 3, I don’t particularly care for the crew. Also the reset button at the end of the episode made me feel like the 45 minutes didn’t matter.