
Picking right back up... Scully is on the phone with Mulder, but is also in her hotel room with 'Mulder'. He's finally got a hold of her and all he gets is a distant 'No, sorry'; he must be having a serious WTF? moment here. Scully told him she thought she was in danger; now he knows it and hauls ass to the motel.

How exactly does she know the one in her room isn't the real Mulder? Hard to say. Maybe you can just tell. Maybe she has scary good instincts. Either way, she pulls a gun on ABH dressed as Mulder, but he throttles her and throws her through a table!

The real Mulder arrives with Samantha, and it's shades of Duane Barry all over again. Mulder seems too shocked to believe it. He becomes panicked again; he's already lost her this way once. He even becomes short with his 'sister', especially when she tries to calm him.

Samantha: I know this is hard for you, Fox...
M: No, it's not hard. It's unbelievable.
Samantha is sure Scully is unharmed; ABH is only trying to get to her. She also describes to Mulder the story behind what is happening with the clones. I'll let her explain:
Samantha: The men you've been seeking are the progeny of two original visitors, clones who have been attempting to establish a colony here since the late 1940's.
M: A colony?
Samantha: Loosely. The community, by necessity, is dispersed. There are clones identical to my parents living in virtually every part of the country... It's their belief that our stewardship of the planet is being forsaken, and that by default, they'll someday become the natural heirs... Through hybridization, they've been working to erase that aspect which has forced the community to scatter... their identical natures.
M: All the clones worked in abortion clinics, why?
Samantha: Access to fetal tissue. Though the biologies are incompatible, they finally found a way to combine human DNA with alien DNA... The experiments weren't sanctioned. It was considered a dilution of their species, a pollution of their race. So a bounty hunter was dispatched to destroy them and terminate the colony.
There you have it. Mulder doesn't necessarily believe her. He finds her sudden appearance in his life to be far too suspicious. Not to mention, now that Scully's been taken again, he's more likely to lash out against everything and everybody, and even less likely to trust people.

Suddenly Skinner shows up. Mulder and Samantha suspect it may not actually be him, so she hides behind the door with a sharp tool while Mulder turns the lights off. Fortunately, it's not ABH- Mulder begins to explain things but the phone rings.

A pulverized Scully is on the other line with instructions from her captor; he wants to make a trade. Scully has no idea who she is being traded for, and Mulder doesn't tell her. They only have an hour before they have to meet. That's not much time to arrange for help, but luckily Skinner is ready for action.
Their intention of course, is not to make a trade, but to take ABH out with a sniper- base of the neck, the only way to kill him. They must be very precise.

That's not what happens. The trade is made; a frightened Scully heads for Mulder's car and sinks below the dashboard. I can imagine she's had quite enough of this life-threatening shit.
Samantha tries to fight back with her neck-piercing tool, but isn't strong enough. What's more, the sniper loses his shot; he fires anyway, sending both ABH and Samantha over the edge of the bridge.
Mulder cries out her name, and Scully finally realizes who she was just traded for. This is no small thing. Mulder has been searching for his sister for his entire adult life; she has been his motivation for everything. And he just traded her for his partner. Unthinkable.

The next morning, Samantha still hasn't been found. Mulder talks as if he's hopeful, but even he knows he's deluding himself. Scully, recently discharged from the hospital is full of questions.
S: Mulder, why didn't you tell me on the phone that it was her?
M: I couldn't tell you.
S: Why not?
M: Cause you'd never let me go through with it.
You've got that right. Scully then wonders if he's sure that was his sister, and Mulder becomes incredibly angry. Even though he himself was doubting her last night, he needs to believe this really was Samantha. Scully reminds him that back at the hotel, ABH looked exactly like him, but wasn't. They can no longer be certain that anyone is who they say they are.
S: Well, then who is this man and what does he...
M: (without hesitation, no room for argument) He's an alien.
S: (pauses) Is that what you're going to tell Skinner?
M: I already told Skinner, that was the easy part. Now I've got to tell my father.

It's almost hard to watch the scene where Mulder tells his father. Mulder is so emotional and his father is so harsh. Of course he's furious! As if their relationship wasn't tenuous enough- I'd probably never speak to Mulder again if it were me. Not just losing Samantha but trading her on purpose for a work associate? Can you imagine?
Bill Mulder: Do you realize what losing her again is going to do to your mother?

Such a serious guilt trip, though, as if Mulder wasn't feeling bad enough as is. Mulder cries and apologizes over and over. Bill Mulder hands his son an envelope, saying it was from Samantha. 'in case we get separated, meet here'.
"Here" is the clinic where her clones are. Before Mulder passe through the gates, however, he gets a call from Scully. Mulder explains the letter and tells her he believes Samantha is alive. Watch him go from hopeful to being totally crushed as Scully tells him otherwise; they just pulled her body from the river.

He's not sure what to do next. He tells Scully he'll be right over, but instead he chooses to check out this clinic while he's there. Maybe she'll be in there after all.
As it turns out, she's in there several times over.

There are many copies. And they have a plan.
Mulder is shocked to find the truth, but even more so, he is so furious. How could they use him like this? Play with his emotions, and make him believe his sister had come back to him? For this unforgivable sin, he basically tells them to go to hell.

He refuses to protect them. In a last ditch effort to get his help, they tell him the real Samantha is still alive and they know where is is. How else would they know so much about her? The truth, we'll find, is that they were lying to him. Samantha died when she was still a girl (but we won't know for sure until the seventh season).
So ABH finds them and kills them. He leaves Mulder alive, but sets the clinic on fire.
This makes Mulder more determined than ever to figure out just what exactly is going on here. I'm not sure how he contacts X, but Mulder interrupts his night out.
M: How was the opera?
X: Wonderful, I've never slept better.

LOL
M: I need to know what you know.
X: Okay. They're all dead.
M: No. One of them is alive, the one who was sent to kill them. Where is he?
X: A nuclear submarine located his craft in the Beaufort Sea five days ago. They were ordered to destroy it but they were disabled. An attack fleet left port from Anchorage this morning to make sure this man does not leave.
That's enough for Mulder. Off he goes.
Meanwhile, Scully finds out why alien blood is toxic to humans;
GARDNER: Apparently. When the body's exposed to it, it triggers a massive production of red blood cells. Now, take a look at this. We took a second culture and were able to control it's growth.
S: What did you do to it?
GARDNER: All we did was lower the temperature by five degrees Fahrenheit.
S: So the virus is inhibited by cold.
Keep that in the back of your mind for future eps; I'm definitely curious about continuity on that one (Fight the Future, I'm looking at you!)
Scully goes over to Mulder's apartment to bring him up to date on what she knows. She notices two newspapers stacked by his door, obviously surprised to see that Mulder has already been gone for at least two days and she didn't even know it! She thought Mulder was just taking some time off because of his sister's apparent death.
When she goes inside to figure out what's going on, she finds a message for her.

M: Scully, when you get this message, I will be too far away for you to stop me, but where I'm going I cannot allow you to follow. I won't let you jeopardize your life and your career for reasons purely personal to me. You were right, Scully... you said a line has to be drawn somewhere. I'm drawing it for you here. I'll contact you when I can.
She can't believe what she is reading! Mulder has gone off to do something that he clearly believes could endanger his life. And she's not invited. Scully finally knows what it's like to be on the other end; the determined to rescue, somewhat panicky end.
Fearing for Mulder, she goes to Skinner for help; she knows he's connected to people that she simply is not. She meekly enters his office when his assistant is away from her desk. She tells him Mulder is gone, and asks if he can help her find him... through unofficial channels.

Skinner considers this for a moment. This is tricky, because agreeing would mean admitting his dubious connections. Of course he will help her, because he cares about both of them, but just as in One Breath, he needs to make it look like he has nothing to do with it. More than that, he needs to save face at the office- who knows might be listening!
Skinner: He's risked my position, your life.
S:(emphatically) Agent Mulder has saved my life!
Scully always defends him. Feeling a little discouraged, Scully heads back to Mulder's apartment. She finds the masking tape X on the window, with a lamp propped up beside it. Easily putting two and two together, she turns on the lamp, and then falls asleep on Mulder's couch waiting for a mysterious informant to arrive.

When he does, X steps into the door frame without looking. When he realizes Scully is the one standing there, he pretends he's got the wrong apartment. Scully all but loses it on him, as he continues to pretend not to know anything. Scully, not knowing what else to do, really, goes back into Mulder's apartment. X takes the elevator back downstairs.
But Skinner is waiting for him, like the intimidating horror movie villain he should be.
Battle of the Badasses ensues!! Answering the age old question; "Why doesn't Skinner just beat the information out of him?"

Damn I love this show. Skinner gets his info. He appears at Mulder's door all bloody and tells Scully everything she needs to know in order to rescue Mulder.
Which is great, because by now, Mulder could do with some serious rescuing. He's found ABH, but I bet he wishes he hadn't because he's getting pummeled. He begs ABH to tell him where his real sister is. Not that ABH would know, so he messes with Mulder and tells him "She's alive. Can you die now?"

Mulder manages to shoot ABH in the neck, but it wasn't in the right spot, so Mulder is blinded by the toxic blood and thrown out. That's how he managed to be in the condition we first saw him in, when this whole mess started.
Scully managed to track him down, and now is responsible for reviving him. The hospital crew is skeptical to say the least, but eventually Scully cons them into going along with it. She is frantic to save him, and totally gutted to see him this way.
She administers the defibrillator paddles, which to me almost seems like an act of violence to a person's body. What a scary thing to do, but totally necessary. Scully yells orders at the hospital crew but the doctors is seriously unconvinced this is going to work, even suggesting they give up.
DOCTOR: This patient's not even in...
S: (emotional but determined as hell) He's going to make it.

Scully runs her fingers through Mulder's hair. She's just going to will him to live. After blood transfusions and anti-virals, Mulder improve a bit. He lays unconscious for days, and Scully sits and sits waiting for him to wake up.

She doesn't even change. She probably didn't even pack, just got on a plane as fast as she could.
She seems to remain fearful until Mulder finally wakes up; then she positively glows.

S: Hey! How're you feeling?
M: (barely able to whisper) Like I got a bad case of freezer burn.
S: (just teasing) Thanks for ditching me.
M: (wide eyed and genuine) I... I'm sorry, I... I couldn't let you risk your life on this.
S: Did you find what you were looking for?
M: No. No. But I... I found something I thought I'd lost. (Scully tilts her head 'what?') Faith to keep looking.
Scully smiles at this.
< / End Game >