Mulder (David Duchovny) is no longer an agent on the X-files, or even working for the FBI anymore, Scully (Gillian Anderson) is taking her maternity leave, and Doggett (Robert Patrick) is left to run the X-files, alone….

Written and directed by Frank Spotnitz, this episode first aired on 6 May, 2001, and despite the title, we soon learn that Doggett won’t be alone, at least through this episode. He’s introduced to a new partner, Leyla Harrison (Jolie Jenkins), who transferred in from accounting, because she’s been a fan of Mulder and Scully’s work over the years (this is very much a nod to the fanbase, their knowledge, and their questions about the series).

Harrison brings Doggett a strange case from New York that relates to some strange reptile attack. As the pair investigate, they soon find themselves trapped in an underground complex of tunnels hunted by a strange reptilian creature. Skinner (Mitch Pileggi) asks Mulder to consult, and Scully does some forensic work on the victim of what is initially believed to be a murder.

All of them end up working on their own, but all towards a common purpose.

Harrison knows her subject matter, but may not actually be cut out for the work, and Mulder, despite getting caught up in the case, reminds Scully that there are more important things to worry about right now.

This one is fun, and satisfying, as we get a lot of nods to previous episodes, whether through Harrison, or from Scully packing up for her leave. It also works very well as a monster of the week episode, and ends up being a little creepy.

Essence was written by series creator Chris Carter, and picks up the mythology thread tying into Scully’s baby, the alien invasion, and the slowly brewing super-soldier angle. It first aired on 13 May, 2001.

Whatever Billy Miles (Zachary Ansley) is, it’s back. He/it has destroyed Zeus Genetics, which popped up a few episodes back, relating to Scully’s pregnancy and the belief that they may be helping pregnant women bring alien babies to term. And we learn that they were doing it for the express purpose of cultivating cells and material for research and application.

A nurse, named Lizzy (Frances Fisher) is helping Scully out around the apartment, but she may have an ulterior motive and plan, as it’s revealed she’s working with Duffy Haskell (Jay Acovone), who was involved in protecting pregnant abductees, and their involvement with Zeus Genetics.

All of it centers on the fact that they (the aliens?) don’t want Scully’s baby to be born, for what it may represent – a divine intervention, an implication of more human than human – whatever it is, they seem to be afraid of it, and they, through Miles are targeting Scully – but once again, this conspiracy may be more far-reaching than they believe.

Even as Mulder and Doggett call in all hands to help protect Scully and get her out of the city, including Reyes (Annabeth Gish), they are all delivered a reveal on who is now working on their side…

As Skinner and Mulder deal with Billy, we learn that Crane (Kirk B.R. Woller), another FBI agent, may be more than he appears, and Scully and Reyes race towards a To Be Continued, and a season finale, where we are left wondering who to trust (no one) and the belief that the truth is out there…