Warning! Plot details!
In X-Seven, a long-standing conflict between Overseers and Interventionists was shown to be reaching a climax. The main Interventionist agent is Gary Seven. Over the years, Dana Scully has become caught up in several of Gary's tricks for introducing new technologies to Earth and she is now aware of the struggle between Gary and Rupert. Rupert is the top agent being used by the Overseers in an effort to reveal Gary's illegal interventions into the development of human culture on Earth. At the start of Moon Reyes, Rupert is returning Gary to Moon Base with evidence that Gary has illegally introduced advanced genetic engineering technology to Earth.
In the past, Gary has worked to prevent nuclear war and limit the impact of Global Warming. Now his efforts are centered on completing a plan to provide humans on Earth with a key technological advance that will greatly accelerate research into the creation of artificial robotic life with human-like intelligence. During the past 40 years, Gary has been aided by Roberta, an Earth human who accidentally learned that Gary, although a human, is actually from a distant star system. Similarly, FBI agent Monica Reyes has been thrust into a similar role. Monica's investigations of Scully's abduction has twice resulted in her capture by human agents based on the Moon. At the start of Moon Reyes, Monica is going to the Moon for the second time and Gary is planning how to use her as an interventionist agent.
Initially Gary thought to place his own mind control nanites in Monica and use her as a way to get at Skinner. Skinner's knowledge of Observer activity on Earth would complicate Gary's plans. But Gary quickly crafts an alternative plan (replacing Monica within the X-Files office with Keri Anne Wold) that involves letting Rupert make use of Monica and using another method to gain control of Skinner.
In an effort to find Monica, FBI agent John Doggett is investigating the employees of Champion Research. Some of the employees have disappeared and the others claim to know nothing about who was in charge of the bacterial bioengineering project that Scully worked on in Mexico. Doggett is not surprised to find that the employees show signs of memory disruption similar to that suffered by Monica after her previous abduction.
Doggett is assigned a new partner, Keri Anne Wold, who has advanced degree in electronic engineering. She starts reading through the X-Files in her spare time and notices an unexplored lead from an abandoned investigation of unexplained material found at the Flight 93 crash site. Skinner moves them off the Champion Research investigation and assigns Doggett and Wold to further investigate unexplained circuits from the Flight 93 crash.
Doggett continues working to find Monica with the help of Mulder and Scully. Finally, Gary has to step in and adjust their memories. Gary has barely escaped being ejected from the Solar System for his involvement in the bacterial bioengineering project. He was helped by a robot on the Moon who managed to steal the key evidence (the bacterial samples) from the Overseers. Now Gary must act in order to keep Doggett, Mulder and Scully from making known additional evidence that branched DNA was used to make the carbon-trapping bacterial strain that he has allowed other scientists to "discover".
Continuing his efforts to trap Gary in illegal activity on Earth, Rupert intensifies his efforts to show that Gary has been teaching humans on Earth how to manufacture components for advanced robots. Rupert and the Overseers make use of Monica as a trained investigator to find the source of the robot components that were found at the Flight 93 crash site (Rupert stole the original evidence to keep Earth humans from learning anything from it). He tells Monica that she can help prove that Gary's robot was involved in the events of 9/11. Gary has carefully constructed the appearance that the illegal robot work has been conducted by Cognite Systems in San Carlos, Ca.
All investigations converge on Cognite Systems and Gary is convicted by the Overseers of illegal intervention. Gary and Roberta retire. The real robot manufacturing operation on Earth continues undetected. Keri is actually Gary's sister, and she continues Gary's work. Reyes returns to the X-Files with Doggett. Mulder and Scully continue as before.
I'm thinking that Monica is going to participate in an Interventionist operation on Earth (think Patty Hearst) and be trying to manipulate John (and his new partner) while trying to double-cross the Interventionists. John will be forced to work on an assignment that he is uninterested in, but he will eventually learn that it leads to Monica. Once Monica and John are back together they are going to have revenge for Monica's abductions.
Maybe the clones can be trying to gain access to Skinner so they can manipulate his memory. They put Monica on some other "dummy mission" while using her presence on Earth to set a trap for Skinner.
Gary Seven will be trying to help Skinner (in order to work against the clones). Also using Roberta to feed Doggett clues about the case he is on, so he can figure out it is a cold "clones case" and actually leads to the current location of some of the clones (and Monica).
"cold case": several years previously (okay, this has to be the unexplained teaser for Part II) Gary Seven is on Earth trying to prevent the September 11 attacks. The clones foil his attempt to do so, but leave behind some key evidence of how they operate on Earth.
Doggett and Keri are initially assigned a new X-File case dealing with the theft of some Sept. 11th Commission documents. (Some funny report of Roberta "magically" getting into a high security document storage facility.) Then Roberta shows up at John's house with the documents and tries to get him to understand how they are related to the clones and Monica.
need to explain how Roberta's association with the Marine Science Institute was faked by Gary Seven.
Moon Reyes continues with what happens in the space ship as Monica, Gary, Isis, and Roberta discuss earth observation, Observers and Interventionists.
Monica: memories are reactivating from previous visit to the moon. Battle in her brain between nanobots from the clones and nanobots from Gary Seven. Monica has only sketchy memory of how she got on the ship, starts to trust Roberta and the interventionists mainly as an intuitive choice over the observers (clone brothers). Monica wants to understand everything about both factions and find a way to return to Earth with her knowledge intact. She is particularly interest in learning more about Roberta and why she, as a native of Earth, is willing to work with the interventionists. Once back on Earth, Monica tries to get messages to Doggett that only he will recognize- she does this indirectly through emails to his new partner and by mentioning things like Doggett getting an office assistant of the month award.
Gary Seven is involved with a plot to infiltrate his sister into the FBI so as to be positioned to reveal the workings of the Observers on Earth. The ultimate goal is to introduce nanotechnology to Earth without being caught. The plan is to set a trap that will allow Earth humans to capture nanotechnology from an Overseer who is called into action on Earth by the clone brothers. Reyes is to be the tool used to set this trap. Gary is allowing himself to be “deported” by the overseers upon reaching the moon, to make it look like his ring of interventionists is falling apart.
Roberta, in order to play her role in the trap, is not being informed by Gary and Isis about what the plan is. Roberta knows something is up and dislikes having to work in the dark. Her resistance to Gary is being played up in order to make the clone brothers think that she is willing to break with Gary and help the overseers/observers finally trap Gary Seven’s brothers and sisters. The observers are convinced that Roberta can help them trap the rest of the Gary Seven clones. This leads to the operation set up on earth for producing robots (passed off to Overseers as attempt to give nanotech research boost to Earth..
Isis, as a nanotech life form that should not be on Earth is also deported along with Gary right after reaching the Moon at the start of the story.
Scully is able to talk with Mulder about things he remembers from being abducted. Scully tries to make a report to Skinner, but he is under a tight nanodevice brain implant control placed by the Observers. Scully returns to her job with increasing nanobot implant-induced disinterest in her DNA, her trip to the Moon, and her experience with Roberta in Mexico. Mulder continues to try to gather evidence about the observer clones, including using the Lone Gunmen to help keep tabs on what the FBI is learning from their database of clone sightings.
Doggett is assigned to work with a new FBI special agent who is actually the sister of Gary Seven. This is not revealed until the end of the story. The interventionists have arranged to have one of Gary Seven’s brothers work in the FBI crime lab. He reports strange shit in the flight 93 debris and after all else fails, it becomes an X-file and Doggett and his new partner are assigned to the mystery. Doggett does not want to work on this new case, leaving his new partner to do it.
Doggett continues to investigate the company in Calif. that was involved with the Scully operation. Finally Doggett’s new partner shows him security images that indicate Gary Seven (not under that name) was a ticketed passenger for flight 93. Doggett has a haunting fragment of memory of seeing Gary Seven in Mexico abducting Monica, so he suddenly gets interested in the case. But it turns out that his work in Calif. is what allows him to figure out the connection between the two cases. This leads them into the trap that the observers have set to catch the Interventionists giving tech to humans which is really a trap set by the interventionists to make the FBI aware of the Observers. Everyone come together and the observers revealed for what they are to Skinner and FBI, and the FBI gains nanotech detector (can detect brain infiltrating nanodevices), forcing human Observers and Interventionists (equipped with nanodevice brain implants) off of Earth. This detector used the kind of technology developed for bioterror detectors that Scully is working with (allows to bring her into the end story) All of Mulder’s nemisi (clones) depart, leaving him without his prey.
The interventionists are left with their robot agents on Earth (which the Observers are unaware of) while the Observers continue observing by with robotic sensors (insects, etc)
Doggett and Reyes are reunited, Doggett’s new partner is now detected as being a Gary Seven clone (morphable face, etc), but all of the Observers, Overseers, and Interventionists are extracted from Earth except her. She goes into prison, but is sprung by interventionist robots who ask Monica for help. John knows that she did it, does not really understand why, but agrees to trust her and not turn her in for the jail break. The End.