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Episode 1X79: The X Files - The Pilot
Mulder and Scully meet for the first time. Although they don't hit off straight away, Scully is very willing to strip to her underwear to show Mulder her "marks" (actually insect bites).
Scully was intended to have a boyfriend in this episode called Ethan Minette, and it would have been interesting to see how long he remained in the show. Would they have ever got an episode with him getting jealous and attacking Mulder? Who knows?
Episode 1X04: The Jersey Devil
Scully decides she wants a life outside work, having possibly been put off Mulder when she walks into his office and catches him reading a porn magazine. Rob, her date, turns out to be a rather tedious person, and she decides to quit with the dating for the time being.
Episode 1X11: Fire
Mulder meets his old girlfriend, Phoebe Green, and Scully is clearly jealous - especially after she witnesses the two of them kissing in the hotel lobby. However, Pheobe turns out to be a cheat - having an affair with the equally dislikeable Sir Malcolm Marsden.
Episode 1X14: Lazarus
We learn that Scully previously dated Jack Willis. But he dies, so that won't go a long way. Mulder also makes a point of the fact that rescuing Scully is very important to him - showing how much Scully means to him.
Episode 1X20: Tooms
Scully brings him some food while on their stakeout and actually tries to get close to him - calling him "Fox". His reply isn't the best of responses - "I even made my parents call me Mulder". Scully's no doubt thinking "Is he crazy?"
Episode 2X01: Little Green Men
Scully gets blown off by Mulder when they pass in the corridor, and has to resort to almost covert measures to get to see him.
Episode 2X07: 3
Despite his fling with Kristen Kilar, Mulder also engages in the wearing of Scully's cross necklace throughout the episode. He's just confused, I guess.
Episode 2X08: One Breath
Mulder makes his feeling towards Scully very clear with his anger towards the doctors and, later on, Cancer Man.
Episode 2X11: Excelsis Dei
When Mulder and Scully question Hal Arden, he shows them his unmentionables and then comments that he "didn't mean to tread on your toes" to Mulder, having clearly thought the two were an item.
Episode 2X13: Irresistible
One of the first examples of Mulder actually trying to do something outside of work with Scully. He gets two tickets for them to see the New York Knicks game. Sadly, they have to cancel after Moe Bocks finds more bodies (all Donnie Pfaster's fault). Mulder hugs her when he saves her life.
Episode 2X16: Colony/Episode 2X17: End Game
In a reversal of the roles in One Breath, Scully is clearly very concerned about Mulder, while he does his best to protect her.
Episode 2X19: Dod Kalm
Mulder becomes very dependant on Scully while dying of old age, and they do a lot of snuggling up. They love each other too much to be able to finish the water that Scully has found.
Episode 3X02: Paper Clip
Mulder and Scully get very close - again - when Mulder comforts Scully over Melissa's death.
Episode 3X10: 731
Oh dear. Mulder and Scully's relationship seems to be taking a downturn here, with Mulder becoming consumed with anger over the recent events.
Episode 3X12: War of the Coprophages
Having gone off Scully recently, Mulder pursues Bambi Berenbaum from the moment they meet, only for her to show more interest in Dr. Ivanov. Smart is sexy.
Episode 3X13: Syzygy
Although a lot of the problems are the effects of the cosmic alignment, Mulder and Scully are definitely at odds. Mulder shows an interest in Detective White, and mocks Scully mercilessly, while Scully becomes even more insecure about the other woman.
Episode 3X17: Pusher
Mulder and Scully start to put previous events behind them, and they certainly seem to be getting on very well while looking over Modell's comatose body.
Episode 3X22: Quagmire
Mulder and Scully share a long heart-to-heart conversation while "stranded" on Heuvelman's lake.
Episode 3X23: Wetwired
Another banana skin, after Scully is brainwashed and thinks Mulder is out to get her. Luckily, Mulder is able to restore her trust in him by the end of the episode.
Episode 4X01: Herrenvolk
Like with Melissa's death, Scully hugs Mulder and comforts him when it looks like Tena Mulder will not recover.
Episode 4X03: Home
Mulder's reference to a man with "spotless genetic makeup" with whom she can start "pumping out the uber-Scullies" sure sounds like himself.
Episode 4X05: The Field Where I Died
Mulder and Scully were together in their past lives. Maybe it's a sign.
Episode 4X13: Never Again
Mulder blows it again, by bordering on the authoritarian, and declining to tell Scully where he's going (right, Elvis' Graceland Suite is too personal to tell the woman who loves you?)
No wonder, Scully has a one night stand with Ed Jerse. She even undresses in front of him!
Episode 4X15:Memento Mori
Scully becomes very defensive over her cancer, but Mulder is clearly concerned. He shares a very touching moment with her by hugging her and kissing her forehead.
Episode 4X17: Tempus Fugit
Finally, Mulder and Scully do something outside of work - Mulder takes Scully out for her birthday. Agent Pendrell is also infatuated with Scully, and she regrets not getting to know him better after he dies.
Episode 4X20: Small Potatoes
Scully seems more than willing to entertain "Mulder" (really Eddie Van Blundht). She's certainly surprised when the real Mulder comes crashing in.
Episode 4X22: Elegy
Mulder loses it with Scully, when he finds that she kept the fact that she saw a ghost from him. It looks as though their relationship took about three steps back.
Episode 5X02: Redux
After faking his own death, Mulder hides in Scully's apartment and starts watching her undress. Stalker.
Episode 5X03: Redux II
Mulder is concerned about Scully, and the hospital staff are far from helpful. Bill Scully fails to notice his concern and blames him for everything, but Mulder cries by Scully's bedside.
Episode 5X04: Detour
Mulder and Scully sit in the back seat of the car together when on their way to the convention, and Mulder and Scully share some food in Scully's motel room, despite Scully's silly comments about the rules against consorting. But, when trapped in the woods, their relationship certainly begins to grow, with Mulder inviting her to climb naked into a sleeping bag with him, and Scully singing to him.
Episode 5X06: The Post-Modern Prometheus
When at the Cher concert, Mulder asks Scully to dance. She accepts.
Episode 5X07: Emily
Mulder is the first person Scully calls regarding Emily. You can see he's keen to be this girl's foster father. Unfortunately, their first (unofficial) child ends up dying.
Episode 5X11: Kill Switch
Most of Mulder and Scully's interactions are far from romantic, as Mulder becomes frustrated with his partner's skepticism. When in virtual reality, Mulder is saved by the gorgeous, femme fatale nurses, by Scully. But in one of the most disturbing moments I've seen, he actually kicks Scully. Just as well none of it is real.
Episode 5X12: Bad Blood
Mulder and Scully are a little more back to normal. Mulder is clearly jealous over the sheriff, by imagining him as being a buck-toothed moron.
Episode 7ABX18: Hollywood AD
Okay, I'm getting a bit ahead of myself, but I genuinely believe that most of this episode took place at this point in the timeframe. During the latter half of 1998 (18 months before the time of the end of Season 7), Mulder and Scully were off the X Files and not even allowed to talk to Skinner. Had their investigation taken place any later, Mulder would not have even been around to watch the movie (or at least, Scully would have been heavily pregnant).
Scully spends some extra time with Skinner, leading Wayne Federman's overactive imagination suspect that Skinner and Scully have a thing going. Mulder takes Scully out for lunch in a coffee shop, and Scully tells him all about "Sister Spooky". After Skinner suspends them, they start seeing each other out of work, watching Plan Nine From Outer Space together, and going to see the making of "their" movie.
Episode 5X17: All Souls
Scully calls Mulder "in an unofficial capacity". They're possibly still serving their suspension after their bungling of the case in Hollywood AD.
Episode 5X18: The Pine Bluff Variant
Sadly, after all the film watching and inviting each other out to dinner, Mulder and Scully's relationsip starts to go into freefall when Mulder is forced to keep his undercover activities a secret from Scully. A suspicious Scully trails Mulder until Skinner tells her what is going on. Scully perseveres, even though Mulder's first instinct is to try to chuck her out of his apartment (after his actions in Redux, this seems rather hypocritical). Luckily, Scully manages to calm him down, putting a bandage on his finger.
As is too often the case, Scully only realises her true feelings for Mulder when it appears that she can't have him any more. After she sees him holding hands with Diana Fowley, she has to go and think about it for a long time. She later hugs him in their burnt out office.
The X Files: The Movie
Forgetting all about Fowley, Mulder makes a move on Scully - but is thwarted when she collapses. He gets a look at her while she's semi-naked when he goes to rescue her.
Episode 6ABX01: The Beginning
Mulder and Scully's relationship is in trouble again, as Mulder explodes at Scully for not backing up his story about the UFO. He ditches her in favour of Diana Fowley, but appears to come to his senses when she betrays him.
Episode 6ABX03: Triangle
Mulder travels back in time and meets 1930s Scully, and immediately starts trying to make a move on her. Inevitably, the two of them eventually begin running through the Queen Mary together, and he decides that he could at least try and make a move on her, only to be punched in the face. When Mulder tells Scully he loves her, she is still rather miffed about Fowley, and tells him: "In your dreams!"
Episode 6ABX04: Dreamland
Mulder seems to be oblivious to the subtext behind what Scully's trying to tell him in the car. She wants to get a room together, Mulder! Of course, he is uncomfortable with the idea of sleeping with Morris Fletcher's wife, and says Scully's name when waking up.
Joanne assumes "Morris" and Scully are having an affair, and Morris clearly thinks Mulder's a fool for not actually trying it on with Scully - his passes at her leading her to suspect he's got brain damage. Of course, he's also a player, going after Kersh's secretary too.
Episode 6ABX05: Dreamland II
Morris Fletcher decides that "all of that is going to change", and does what Mulder should have done a long, long time ago - he invites her round for dinner. By now, he's behaving so oddly that Scully figures out this is not Mulder. Scully seems desperate when it looks like this will be the last time she sees her partner.
Episode 6ABX07: The Rain King
Another bunch of people who think the same way as the late Hal Arden - Mulder and Scully are mistaken for a married couple who won a prize to look around the Kroner weather studios. As Mulder notes when he sees the elderly couple: "It's like looking at a mirror image". Scully faces even more competition from Sheila Fontaine, who gives Mulder a huge kiss.
Episode 6ABX08: How the Ghosts Stole Christmas
Mulder wants to go ghost hunting - and he chooses to do it with the one woman he truly loves - Scully. After escaping, Scully snaps out of her denial and goes round to Mulder's house to exhange Christmas Presents with him. Finally.
Episode 6ABX12: One Son
Mulder and Scully's relationship hits the rocks, because Mulder can't forget about Fowley. Scully really needs to slap him when he tries to stop her interrogating Fowley, and after he ridicules her in front of the Lone Gunmen, she's finally had enough. Fowley makes her move on Mulder, by kissing him. Booooo! Hissss!
Episode 6ABX13: Arcadia
Mulder and Scully are back on the X Files (despite the transmission order, dialogue makes it clear that this is next chronologically after One Son), and posing as a married couple. Despite the fact that they're clearly very comfortable with this, Scully is still angry over her partner's behaviour in the previous episode and won't sleep with him. Serves him right.
Episode 6ABX15: Monday
When Mulder is mortally wounded, Scully cradles his body. Of course, this never really happened.
Episode 6ABX16: Alpha
Scully must be wondering how many women Mulder has in his life, when it transpires that he's been communicating with Karin Berquist via e-mail. She is killed, but thinks enough of Mulder to leave him an I Want to Believe poster in her will.
Episode 6ABX18: Milagro
After all the rejection from Mulder, it's probably not surprising that Scully seeks solace with Philipp Padgett. Mulder hugs her after finding that she's alive after almost being killed.
Episode 6ABX19: Three of a Kind
Scully will do anything for Mulder, going up to Las Vegas because she thinks he's there.
Episode 6ABX20: The UnNatural
Scully makes more advances on Mulder, suggesting (implicitly) that they go out for the day and enjoy themselves. Mulder finally takes the hint and invites her out to play baseball with a ghost (yes, that kid is definitely a ghost - or has discovered the fountain of youth, and hasn't aged in 50+ years). He holds her close to him as he shows her how to swing the ball.
Episode 6ABX21: Field Trip
Mulder and Scully are rescued from certain death, and hold hands in the ambulance.
Episode 6ABX22: Biogenesis
Fowley tries to drive a wedge between Mulder and Scully, (evidently) sleeping with him, and trying to stop Scully seeing him. When he goes crazy, he calls for Scully.
Episode 7ABX04: The Sixth Extinction II: Amor Fati
Mulder's dream is full of symbolism, as he realises that marrying Fowley would be the wrong path to take. Scully appears to him and calls him a deserter. Fowley realises that Mulder and Scully belong together, and allows Scully to rescue her partner, being apparently killed as a result of betraying Cancer Man. Scully kisses Mulder on the forehead.
Episode 7ABX13: First Person Shooter
No, I didn't forget about Millennium, but this episode takes place in October 1999. Mulder says he has a birthday coming up. Considering that Mulder is being tortured on an alien spaceship during his birthday in October 2000, and is on the run from aliens in October 2001, this can't really take place any other time. After that, the Lone Gunmen are dead. Unless of course the Lone Gunmen are all solid ghosts who enjoy playing video games.
Mulder and Scully are found laughing in a closet. I wonder what else they were doing (nudge, nudge, wink, wink).
Episode 7ABX18: Hollywood AD Revisited
Mulder and Scully are in denial at the premiere of their movie, showing them having a fully blown romance (this is before the events of all things), and Mulder finally has had enough at the idea of Scully being in love with Skinner. Mulder and Scully go out on a date after the premiere.
Episode 7ABX05: Millennium
Finally, Mulder and Scully have their first proper kiss.
Episode 7ABX11: Closure
More socialising from Mulder and Scully, this time in a diner while they read Samantha's diary.
Episode 7ABX15: En Ami
Scully blows it with Mulder, but it's not entirely her fault - after all, her message to him was intercepted. She's furious when it appears that Cancer Man slept with her, but he does appear to have a thing for her. Mulder goes off her, though.
Episode 7ABX16: Chimera
Scully is angry with Mulder after the events of En Ami, and his call of "no anchovies" doesn't help much.
Episode 7ABX17: all things
Scully and Mulder are still at loggerheads, and she isn't in a mood to speak to him - but after her spiritual experiences, they reconcile by having sex in Mulder's apartment.
Episode 7ABX21: Je Souhaite
Once again, Mulder invites Scully round to his apartment to watch a movie. Aaaah!
Episode 7ABX22: Requiem
Scully and Mulder snuggle up together in one scene.
Episode 8ABX02: Without
While being tortured, Mulder calls for Scully!
Episode 8ABX08: Per Manum
Okay, this is out of sequence, but I really don't know when in the sequence this did happen, but we do learn that at some point, Scully considered getting Mulder to be the father of her child.
Episode 8ABX14: This is not Happening
Scully is devastated over Mulder's "death".
Episode 8ABX15: DeadAlive
Scully's dedication to saving Mulder is amazing.
Episode 8ABX18: Three Words
Mulder is jealous of Doggett, giving Scully the cold shoulder and attacking Doggett.
Episode 8ABX17: Empedocles
Mulder and Scully finally do what we wanted them to do - they become a couple. Mulder comes round to Scully's house to give her presents, and generally dotes over her.
Episode 8ABX16: Vienen
Mulder acknowledges that he is the father of Scully's baby, telling her if he doesn't make it, to tell the kid he died heroically.
Episode 8ABX19: Alone
Mulder and Scully are very much an item, with Mulder taking his
partner lover to her ante-natal class. They hold hands in the hospital.
Episode 8ABX21: Existence
After William is born, Mulder and Scully share another kiss.
Episode 9ABX01: Nothing Important Happened Today
It looks like it is all over, when Scully convinces Mulder to leave - but it's for his own good.
Episode 9ABX08: Trust No1
Scully is in e-mail contact with Mulder and desperate to get him back.
Episode 9ABX12: Scary Monsters
Scully kept a memento of Mulder - his badge.
Episode 9ABX19/9ABX20: The Truth
Scully and Mulder run off together and share a room together. They've lost William to adoption, but in their final scene together, they lie in bed together. I wonder if they'll try for another baby?