Lots of character interactions in this excellent Morgan & Wong script that introduces some very important elements for later: hybridization experiments on abductees.

What happened to Scully

Men of the Syndicate (probably the Overcoat Man and X themselves) leave Scully in the hospital as any vulgar test subject, she's left to recover thanks to the passage of time and her implant, which prevents her from developing cancer (3X09: Nisei). There is no record of her admittance in the hospital. Her status is monitored, through blood samples the Overcoat Man steals.

Scully's experiments involved genetic manipulations. She was part of the hybridization experiments through gene therapy; as many others, she was a failure and but a step towards the successful alien/human hybrid. Byers and the Thinker find never seen before proteins in her blood, the result of "branched DNA" in her own DNA (proteins are synthesized following DNA information). This brached DNA was inserted into Scully's using "technology fifty years down the line [...] The cutting edge of genetic engineering." (Langly). It is alien or hybrid DNA that was made inactive at the end of the tests, now it's only waste product, "a biological poison". At some point it was active though, as proteins based on it were synthesized; Scully had been turned temporarily into some kind of hybrid. "Could be a tracking system." "Developmental stages of a biological marker." "Or something as insidious as grafting a human into something... inhuman." Among all the Lone Gunmen's theories, the latter supporting advaned gene therapy is the correct one. The ET DNA strains were inserted into her aggressively, her immune system fought against this 'alien' intrusion; her immune system is left decimated and Scully's in a coma. The Lone Gunman called 'The Thinker' will be seen in person in 2X25: Anasazi.

Mulder uses an 'X' made of tape and a blue light to call X. But X is unlike Deep Throat and doesn't think as highly of Mulder. "You're my tool, you understand? I come to you when I need you" X uses Mulder only when he thinks it's necessary, when it's possibe for Mulder to expose some of the Syndicate without taking X along with him and in this case X is too involved. What X ultimately gives Mulder is quite telling: an opportunity to take revenge on the men who did this to Scully, to kill them ("The law will not punish these people"). X takes every precaution for not being compromised because of Mulder. "I can’t tell you why she was taken. It’s too close to me." When Mulder captures the Overcoat Man, X must kill him because he'll be able to make the connection between X and Mulder. X takes the body (the body is missing, Skinner: "there is no body"); to the public it's as if nothing ever happened. And to those who knew who the Overcoat Man was it's as if Mulder killed him and X had nothing to do with it: CSM: "I told Skinner you shot the man in the hospital but I didn’t really believe it. And here you are with a gun to my head. I have more respect for you, Mulder, you’re becoming a player!".

Face to face with the Cancer Man

CSM keeps pushing Skinner to calm Mulder down. Reluctantly, Skinner gives away CSM's address to Mulder. CSM gives Mulder a few lies (Mulder: "Why her and not me?" CSM: "I like you. I like her too, that's why she was returned to you") but does let some truth go through: "No wife, no family, some power. I’m in the game because I believe what I’m doing is right.". CSM lives in a Washington apartment, all alone. CSM knowledge of the truth and Mulder's thirst for it is what, predictably, saves CSM's life. The "I’ve watched presidents die" line may or may not make the events in 4X07: Musings true. After Mulder's visit, CSM must have moved.

Character development

Skinner had an out-of-body experience, that makes him somewhat open to the paranormal. Skinner's experiences in Vietnam will be toughed upon again (3X21: Avatar).

We meet Melissa, the whole contrary of her sister (New Age believer). Melissa & Margaret insist on calling Mulder "Fox". Finally, Melissa convinces Mulder to stay at Scully's bedside rather than give way to anger and revenge and, at X's advice, kill those who searched his apartment.

Nurse Owens is Scully's guardian angel; during the episode she interacted with nobody else except Dana. One could think Nurse Owens is a Walk-in (7X11: Closure), taking care of those who suffer.

In 2X07: 3, Mulder turns the calendar to November; Duane Barry's hostage situation was on August 7. Scully's been missing for at least 3 months, but it will be said that she was missing for 4 weeks later in the series (5X07: Emily).

X: "You're a damn schoolboy, Mulder. You have no idea, no idea!"
X: "I used to be you. I was where you are now. But you’re not me, Mulder. I don’t think you have the heart."
X: [shoots the Overcoat Man] "You want to see what it takes to find the truth, Agent Mulder? You want to know what I know?" [shoots him dead]

"Thank you for not smoking" [sign on Skinner's office, ignored by CSM]

CSM: "I’m in the game because I believe what I’m doing is right."
Mulder: "Right? Who are you to decide what’s right?"
CSM: "Who are you? If people were to know the things I know, it would all fall apart."

CSM: "You can kill me now, but you’ll never know the truth. (Mulder hesitates) And that’s why I’ll win. Don’t worry. This’ll be our secret. We wouldn’t want others to start rumors."

Melissa: "Listen. I don’t have to be psychic to see that you’re in a very dark place, much darker than where my sister is. Willingly walking deeper into darkness cannot help her at all. Only the light--"
Mulder: "Enough with the harmonic convergence crap, okay? You’re not saying anything to me."
Melissa: "Why don’t you just drop your cynicism and your paranoia and your defeat. You know, just because it’s positive and good doesn’t make it silly or trite! Why is it so much easier for you to run around trying to get even than just expressing to her how you feel? I expect more from you. Dana expects more. Even if it doesn’t bring her back, at least she’ll know. And so will you."