
There is so much going on in this ep I don't even know where to start. The mythology kicks into overdrive, and so does the UST.
A quick run-down:

Mulder's water has been contaminated, and it's making him violent.
He looses his temper at work, when he thinks he's found his holy grail, only to find the file is essentially gibberish. He throws things and kicks his garbage can! Scully tries to calm him, by suggesting hopefully that it looks like Navajo.

He even loses it on Skinner, not only calling him out on another bullshit assignment (after both M & S complaining about the last two), but taking a swing at him!!! Skinner shows him who's boss.

The authorities call Scully in to discipline her. For, you know, not having control of him or something. Christ Carter makes a gleeful appearance to shed some light on this weird little world he's created.

DIRECTOR 1: Do you have any explanation as to agent Mulder's, bizarre behavior?
S: No sir. Agent Mulder told me he was having trouble sleeping.
DIRECTOR 1: Do you think agent Mulder confides in you agent Scully?
S: Of course, he's my partner.
Chris Carter: Your partner. Weren't you originally assigned to agent Mulder to debunk his work?
S: Yes sir. A year and a half ago. I've been writing regular reports stating the validity of agent Mulder's work on The X-Files.
Chris Carter: Would you lie to protect him?
S: (yes, obviously!) Am I accused of lying?
Notice how she said 'stating the validity' of Mulder's work; not 'questioning' or 'undermining' his work. Even her reports reflect that she's on his side (and secretly she may have come to believe in certain things about aliens).
Mulder doesn't show up at work after his fist fight with Skinner. Scully goes to check up with him at his place; I love it any time she just lets herself into Mulder's apartment. He's sleeping so he doesn't hear her come in- he nearly pulls his gun on her! They have a face off of sorts anyway:

M: I came home. I must be running a fever. Maybe it's the threat of being burnt at the stake.
S: Mulder, you opened the door for them, they're just looking for a good reason now.
M: (sarcastically) Okay, I'll say I'm sorry.
S: Mulder, these files. Who knows you have them.?
M: Why?
S: Because I had to lie today. And I put my job in jeopardy in order to do so.
Mulder tapes an X to his window. Maybe that will help. Scully checks back later that night, but Mulder is gone. Instead, she gets shot at!

Meanwhile, CSM is paying a visit to .... Mulder's Dad!?!? Not only are they acquainted, but they go way, way back... and hint at Mr. Mulder's sinister history. God, the plot thickens. Even more so if you already know that Mr.Mulder isn't actually Mulder's.. dad...

Mr.Mulder has always felt guilt about the 'project', but now there is a good chance he is going to be found out. So he decides to man up and tell his son the truth before he can hear it from someone else. He even hugs Mulder when he arrives, which tells you how bad the news is.
Never gets to tell him though, because this happens:

Sonuvabitch.
I don't think I need to tell you how traumatic this is for Mulder. He does the only thing he can think of; call Scully.
M: I can't leave the crime scene, it'll look like I'm running, make me look guilty.
S: Mulder they're gonna suspect you anyway, you've got no ID on the shooter, you, your behavior has been irrational recently, Mulder can't you see that everything is pointing directly at you?

M: He was shot with somebody else's weapon.
S: Damn it Mulder, you're an FBI agent, you have access to weapons other than your own!
M: All right. Meet me back at my apartment.
S: No. No you can't come home. Someone shot through your window tonight, they almost killed me, they might be trying to kill you.
Mulder is so messed up at this point, he actually falls into Scully's arms when he walks through the door! LOL score!

Scully starts taking his jacket off for him and directs him to lay down, pulling him into her bedroom... LOL double score!

When he wakes up the next morning...

..RST? No, just kidding. Scully is gone; she having Mulder's gun checked out. She wants to clear him of suspicion, but Mulder's still on his violent rampage and yells at her, believing she's become the enemy.
M: What were you afraid that I was gonna shoot you too.?
S: Mulder, I'm being called into Skinners office this afternoon, they're gonna want answers and I'd like some good ones to give them.
M: So you can clear your conscience and your name?! You've been making reports on me since the beginning Scully, taking your little notes!
S: Mulder you're sick, you're not thinking straight, I'm on your side. You know that.
M: Look you have my files and you have my gun. Don't ask me for my trust (hangs up on her).
No telling what Mulder does for the rest of the day. The next scene is at night; he's returned to his apartment finally. Maybe he hit the local bar. He notices Krycek sneaking around.

Krycek is a dead man!
Except... Scully is also on the scene. She tries to convince Mulder not to kill Krycek (though if he killed my Dad, I'd kill him too). Mulder won't listen and Scully... shoots him? What? OMG. Later she explains; "If you killed Krycek with that weapon there would have been no way to prove that you didn't kill your father." OK, I guess.

She manages to get Mulder into a car and drives for 2 days him all the way to New Mexico!! When he finally wakes up, she's fussing over him again, giving him pillows and water.

Check out his face when Scully tells him there was LSD being pumped into his apartment's drinking supply.

We meet Albert Hosteen, who is possibly the most interesting and unlikely return character of all time. I love this guy.
ALBERT: You're lucky she's a good shot.
M: (smiling) Or a bad one.

At this point, M & S share one of those looks that, seriously, (and I don't normally talk like this) you only see on people who love each other. I don't have to mean "Love", but undeniably, there is an effing lot of love in this room. Hell, not only is Mulder not angry with Scully for shooting him, but he actually thanks her for taking care of him! This whole entire ep has been about caring for each other. Looking after each other. Protecting each other. You know, the usual Mulder and Scully stuff.

Scully has to go back right away. In driving unconscious Mulder across the country, she missed an important meeting with Skinner. She'll be hung for this.
S: There's something else. My name is in those files. It appears in the latest entries with Duane Barry's.
M: In what context.?
S: It's not clear, but it has something to do with a test. I want you to find out Mulder. I need you to.
Mulder is left to go check out a buried box car in the desert, filled with alien bodies. The season finale's cliffhanger ending comes in the form of M & S on the phone; Mulder cuts off- CSM has shown up to destroy the evidence and the man who is responsible for its leakage.

CANCERMAN: Nothing vanishes without a trace... Burn it.