Enter three witches...

No, not really. Although I always did want to mimic the best, if you’re going to plagiarize, Shakespeare is probably not the one to pick. Umbra is an astronomy term. It refers, basically, to the darkest part of a shadow caused by a celestial object coming between the sun and the observer. The connection to the story is the shadow world of covert military operations and the "shadow government" that Byers referred to in the first-season episode "E.B.E."

Umbra opens with the murders of some military and intelligence operatives. At this point, we don’t know who the murderer is, just that he’s very good and that the people he’s killing seem to know him. We cut to the head of the Navy’s Investigative Service (NIS, mislabeled: It should be NCIS.), Vice Admiral Jake Karn. Turns out ‘ol Jake’s an old friend of a certain Assistant Director at the FBI, and he calls Walter Skinner to plead for help. Seems that fingerprints purposely left at the scene of the murders belong to a man Jake saw die with his own eyes twenty years ago in Vietnam. So, Jake tells Skinner, basically, a dead man is killing people. Know anyone that can help?

Skinner assigns Mulder and Scully to the investigation. Karn asks that one of his own people be assigned, in the person of one Commander Matthew Stone, USN. Matt’s a big, tall, strapping, handsome fellow. Sparks fly between Stone and Scully, much to Mulder’s chagrin. Mulder, as you can probably guess, doesn’t dig this in a big way, and promptly sets out to dig up as much dirt as he can on CMDR Stone, going so far as to enlist the help of the Lone Gunmen.

Meanwhile, it turns out that the dead man who’s supposedly killing people is Matt’s father. Or at least, the fingerprints are. Scully and Stone head over to the Pentagon to check on Matt’s Dad’s fingerprints. Color them shocked when the prints turn up missing from the elder Stone’s 201 file. Mulder discovers that Matt was flying F-14’s for the Navy during a classified military operation in Libya in the early 80’s when a ground force element of Navy SEALs massacred over 100 children posing as troops. Matt was investigated in a UCMJ Article 32 (roughly the same as a grand jury investigation in the civvie world,) but the charges were mysteriously dropped.

It is also revealed that Stone has been a member of something called a GOBLIN team, which was patterned after the GARNET teams mentioned in the second-season episode "Ansanzi." Assassins, hit squads, call ‘em what you will. It turns out that the people being murdered were all members of Stone’s GOBLIN team, and that they were all on a mission together to assassinate Saddam during the Gulf War, only the mission was called off at the last minute by...you guessed it, Matt Stone. The one remaining member of the team besides Stone, Major Heather Haynes, United States Army, is approached. She has a rather...loud reaction, once she realizes that Scully and Stone are on the verge of playing snuggle-bunnies. She agrees to let the FBI and Stone watch over her in case the murderer makes a try at her.

Which he does. And succeeds, using a variety of highly-technical gadgets that I made up on the spot. Scully and Stone have a nice, quiet lunch the next day or so, and Scully ends up shoving her pistol into Stone’s right eye in an effort to dissuade him from choking her. Turns out Commander Stone is an ice-cold killer who fancies Scully "his" and doesn’t like the fact that Mulder spent the night on Scully’s couch with her in his arms. Scully realizes that Mulder is probably The One For Her.

We then meet Maggie King, who works for the Navy’s Bureau of Personnel (BUPERS,) and is a former lover of Matt’s. She gives Mulder information about Matt, including his rather bothersome habit of killing people that get in his way. We begin to suspect that Mr. Stone has a hidden agenda.

They decide (Mulder and Scully, that is,) to travel up to Groton, CT, where SUBFOR (Submarine Forces) 2 is headquartered so they can speak to an officer currently assigned to the USS Atlanta  (listed in the story as the USS Georgia, ) who served on Stone’s mysteriously lenient Article 32 board. He tells them his fears, although he has no evidence, and points them to another submarine officer that was on the Article 32 board, who happens to be in Pearl Harbor at that very moment.

Mulder and Scully hop a plane to Hawaii, and speak with an old friend of Scully’s father, Admiral Mike Watts. Then they go speak to the sub officer, and come back to confront Watts, who reveals that he’s in on this severe plot to detonate a nuclear or chemical device in Washington to decimate the leadership of the country and take it over in a quasi-military coup. We learn that the ringleader of this merry little band of traitors is none other than Danny Graves, the older brother of Scott Graves who (coincidentally, NOT) was the leader of Stone’s GOBLIN team on the Saddam mission, who we learned earlier was killed on the ground in Iraq by...Matt Stone, in what Stone calls an "accident."

Mulder and Scully head to San Diego to confront Ally Walker, a woman who Watts pointed them towards who is also in on the plot, code-named LIBERTY BELL. While talking with a suicidal Watts on the phone, Scully realizes that the shit is about to hit the fan. Graves shows up in Pearl and kills Watts with his own pistol, making it look like a suicide.

Scully and Mulder interview Ally Roche. Scully threatens to kill her with a poison, and Roche confesses that Graves plans to explode a chemical weapon in Washington, DC. The chemical is named CBX. Ally was providing a Tomahawk missile casing to hold the weapon. Ally is arrested.

Graves sends one of his henchmen, Commander Ronald Ebert, to intercept Mulder and Scully. Maggie King has since joined Our Favorite Duo in San Diego with information she’s stolen from Matt’s apartment. We learn that Matt is on the trail of Graves, and has been for almost fifteen years. The plot has been in existence that long. Ebert shows up, Scully gets the drop on him, and much knife-intensive interrogation results. Ebert decides to switch sides, and agrees to work with M&S. In an effort to hide his machinations, Graves has been using Ebert’s wife as a real estate liaison to purchase his properties. Through some subtle detection, Scully narrows down the three possible sites: Montana, Kansas or Jacksonville, Florida.

Skinner arrives in San Diego, revealing that he is a reserve Lieutenant Colonel in the Marine Corps. (He arrives in uniform, setting of a chain-reaction of Skinner!Swooning the likes of which I’ve never seen.) He also reveals that he is a Guardian, a member of an elite sect dedicated to keeping the world from destroying itself. Stone, also, is a Guardian, although a little lower down the pecking order than Skinner.

Skinner and Ebert go to Jacksonville, Stone and Scully to Montana, Mulder and Maggie to Kansas. While enroute, Ebert tries to kill Skinner. Turns out his loyalties are still with Graves after all. Skinner almost throws Ebert out of the plane, and has him arrested. Ebert reveals that Montana is the location of the CBX.

Skinner, Mulder and King join Scully and Stone in Montana, where Scully is forced to shoot Stone in the shoulder because he won’t play nice with the other children and share his toys. Graves is there, but manages to escape with the CBX. He tells them that he will detonate the device three days hence, on a Sunday, in Washington, DC.

The team, minus Stone, returns to DC to thwart the plot. They go to Quantico to warm up on SWAT tactics. Scully and Mulder, by this time, have become lovers. (In San Diego, when Watts killed himself, btw. Chapter 19 or so, if you wanna go read that part. There’s also some snuggle-bunnies in Chapter 14.)

We discover that Skinner knows more than he’s telling. It turns out that the LIBERTY BELL plan is a plot, all right, but a plot not to decimate the country, but to test Mulder. For what, we don’t know yet, although CSM makes an appearance and starts uttering dire warnings about the end of the world.

Sunday comes, and Mulder, Scully and Skinner chase Graves around Washington, DC and the outlying suburbs, dismantling six CBX devices that were left at various historical landmarks. It is revealed that the CBX devices were all inert, and were placed in such a way as to force Mulder to make decisions as to who would live and who would die, as well as splitting up the team. In other words, Mulder had to send Scully to disarm a device by herself because there was no way for the two of them, together, to disarm all the devices.

Mulder discovers Skinner’s duplicity and threatens his life. Stone reappears and saves Scully from being detained by CSMs henchmen. Graves takes a real CBX device and heads for the White House. Mulder, Scully, Skinner and Stone barge into the White House.

Stone takes a 9mm bullet to the face.

Mulder talks Graves away from the device, and Graves takes Mulder and Scully to Zeus Storage, last seen in "The Erlenmeyer Flask" where we find CSM waiting.

Mulder shoots CSM.

CSM doesn’t die.

It is revealed that CSM is actually an alien, and that he’s 400 years old, and that he’s here to save the planet from alien colonization. He’s been working both ends against the middle, stalling for time, knowing that if the aliens do colonize, no matter what the Syndicate thinks, that will be a Bad Thing. He tells Mulder that he’s (Mulder) been chosen to save the world. That the choice was made before Mulder’s birth, and that Samantha never existed; it was an implanted memory designed to turn Mulder into a haunted, driven man who’s only desire in life was to find the men responsible, reveal the depths of the conspiracy to the light of day, yadda, yadda, yadda. CSM tells Mulder that Bad Things Are Coming, and that Mulder has to prepare himself For What Is To Come. He then turns on the innate psychic ability that Mulder and Scully posses to demonstrate his powers. Mulder and Scully have a few mind-level conversations before CSM turns off the ability (actually, he just turns it down a notch or two,) and the wipes Our Favorite Duo’s memory of the events in the warehouse and knocks them out.

Mulder and Scully come to, return to the White House, clean up the mess, and bury Matt Stone. Maggie is pregnant with Matt’s kid (a sexual liaison happened between them somewhere earlier in the story,) and M&S ask for some vacation time. Two weeks later they return to Washington with suspicious tans on their ring fingers. Various people are awarded medals for the White House crisis, and Maggie gives birth nine months later. Mulder, Skinner and Scully are named godparents.