All canon exists up to and including Je Souhaite, so we know the following:

1. Samantha Mulder died at the age of 14 after escaping from Dominic Savio Memorial Hospital (somewhere in California) in 1979. (Closure)
2. The majority of the 'MJ12' consortium members are dead except CSM and Strughold (there may be others, but we don't know that for sure).  They were killed at El Rico Air Base in 1999. (One Son)

Relationship details:
 
Mulder and Scully finally embark on a sexual relationship at the end of VS 8 and beginning of VS 9 (Devil's Advocate, parts 1, 2 and 3)  Skinner discovers their 'affair' at the end of VS 9 (Justice Interrupted).  Maggie learns of their relationship in VS9 (Mirror Mirror) along with Bill and Tara.  In VS 11 (Great Balls of Fire), Mulder's apartment burns to the ground and he has to move in with Scully.  Later that season, in the season finale/VS12 premiere (Displacement and Dispensation) Mulder moves into a duplex just blocks from Scully's apartment (and closer to the Georgetown U track) and Scully moves in with him.  In VS 13 (At Last) Mulder proposes, at first Scully doesn't accept because they wouldn't be partners, but in the end they declare the wedding vows to each other (alone) and come to an understanding that they are together in every way.  Also in that episode, Mulder gives Scully rights to his inheritance.

I see dead people:

Bill Scully Jr. is dead (Displacement).  Assistant Director Kersh is not dead, but he's been kicked out of the Bureau (Great Balls of Fire).  Tom Colton is dead (Letters, VS8).  Daniel Waterson is dead (Consequences of Our Actions, VS 13)

People who are still very much alive:  All three Gunmen, Suzanne Modeski (who still pines for Byers), Krycek, CSM (or CGB Spender), and Strughold.

MYTHARC for the Virtual Seasons

Circles and Patchwork (VS 10X14, VS 10X15)
Krycek becomes Mulder and Scully's informant about the nefarious deeds of the 'new' consortium.  There is a power struggle between CSM and Strughold, Krycek is on CSM's side (and his own), Charlie Scully is on Strughold's side.  The Consortium, Strughold's side, had, over time, abducted and experimented on a group of women in a small town in New Jersey. 

All the women developed a rare cancer, (Paget's Carcinoma) the same disease Mulder's mother was suffering from when she committed suicide (Seid Un Zeit).  All the women in New Jersey committed suicide within minutes of receiving anonymous phone calls.  When Mulder and Scully find an abandoned Air Force installation with records of the women's abductions, Mulder is shot (shoulder) by Charlie (but Mulder never sees it).  Charlie ties to convince Dana to join him, leaving Mulder behind.  Dana refuses and Charlie knocks her unconscious.  Krycek finds her and gets her and Mulder to the hospital.  When Mulder wakes up she tells him that Charlie shot him and is part of the consortium.

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Last Kiss (VS 10X26) 

Mulder and Scully are in a car accident on an icy road.  Mulder mistakenly thinks Scully has died (due to his own injuries) and stumbles away looking for help.  In the course of going farther and farther away from the road, Mulder contemplates giving up, just lying down and dying to join Scully.  He has a vision of his mother telling him to get up, that there are answers to be found. 

After some convincing on her part, Mulder finally listens to his mother and gets up, heading now for the road and is found.  He wakes up in the hospital to find out that Scully is most definitely alive, thanks to his actions.  Relived, he thinks back to his 'walk' in the woods.  He remembers his conversation with his mother and knows there is something else she was trying to tell him.

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Legacy and Camarilla (VS 10X27 and VS 11X01) 

After investigating a case with a young girl and an abduction journal (bogus), Mulder goes on a rampage to find his mother's journal.  He finally finds it in the Summer House in Rhode Island, but is injected by Charlie (again, not seen), stuffed in the back seat of his car, which is left running in a closed garage. 

Second part of the two-parter is when Scully follows Mulder to Rhode Island and finds him near death.  He is rushed to the hospital with CO poisoning but survives.  Since it was an attempt on his life, Skinner orders them to a safe house where Mulder reads the journal his mother left.  In the journal, she admits to having loved both his father (Bill Mulder) and the man he knows only as CBG Spender or the Smoking Man (CSM).  She also admits that she's not completely sure who is the father to Fox but that CGB is most certainly the father of Samantha.  She also admits that she knew about the 'consortium' because she worked for Strughold as a secretary (which is how she met both Bill and Spender).  She gives Mulder (her son) the 'faith' to keep looking.  In the end, Strughold is upset that the journal is discovered but CSM points out that it's nothing more than a sad telling of one woman's indiscretions and reveals nothing about the colonists or the collaborators, so Mulder is left alone.

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Displacement and Dispensation (VS 11X23 and VS 12X01) 

Bill Scully, Jr. finds long forgotten documents detailing the account of the submarine Zeus Faver and it's encounter with the Black Oil.  He tries to give this information to Mulder, but is killed before the meeting.  Although Strughold and the Scarred Man directed Charlie to 'take care of the matter', it's not known who actually killed Billy boy (Krycek was also a suspect, and it could have been an unknown third party)  In Dispensation, Teena's journal contains a secretly hidden clues that lead Mulder to a man in the desert who takes him to an underground installation run, supposedly, by the military and the aliens.  As Mulder approaches the alien ships in the underground hanger, he is adversely affected by it, giving him a debilitating headache and blurry vision (nothing he can discern)  The installation blows up, but Mulder survives.  His escort turns out to be Jeremiah Smith.

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Finding the Future (VS 12X11) 

Scully's West African biologist friend, Amina Ngebe, has sent Scully another fragment from the space ship the women were examining (during 7ABX03 The Sixth Extinction).  The fragment has a dramatic and dangerous affect on Mulder.  When he first encounters it, he stops breathing and his heart stops.  He is revived by paramedics and transported to the hospital.  While unconscious, he experiences a vision which seems to transport him to another time -- an ancient time.  With repeated exposure to the fragment, he has more and more of these visions, eventually, not needing exposure to send him into a fugue state.  Scully is very worried about him.  The final vision seems to be of the future -- a far distant future.  The world culture which now surrounds us has been laid to ruin, but in its place is a new life, a new culture build up from the ashes of the old.  This vision brings the visions full circle and Mulder wakes up convinced that something big is going down in 2012.  The gunmen theorize that Mulder is becoming an 'ancient alien', but Scully theorizes that he's just becoming more human than anyone else (like in Biogenesis and later in Amor Fati).  In the end, Scully is still frightened by what is happening to Mulder, but she agrees to believe in him.

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Remnant (VS 12 blockbuster movie): 

Mulder continues to have episodes, this time seeing everyone in the Scully family murdered at the park.  Meanwhile, in California, an ancient Anasazi suddenly appears in a shopping mall.  The man is taken by members of the military to be studied.  A geeky lab rat (and friend of the gunmen) at the facility is scheduled to be 'terminated' for his knowledge of the little man, but Krycek saves him at the last minute. 

Mulder has a vision of an Indian Massacre that frightens him, but seems to be telling him something. While Mulder and Scully are investigating the little man's appearance, they discover a security tape showing Jeremiah Smith appearing and disappearing near the time of the Anasazi's appearance.  Mulder theorizes that the Anasazi is a gift from the aliens, that he has something the people of earth need. Mulder and Scully find Krycek and the lab geek.  Meanwhile, in Brazil, Strughold is informed of the appearance by Charlie.  A Scarred man and Strughold confer (without Charlie present). 

Lab geek (Ronnie) explains the appearance of the little man (and validates that he is ancient) to Mulder and Scully.  In the lab, a scientist known as Dr. Behrens is actually Marita Covarrubias and she tries to figure out a way to escape with the Anasazi.  It's revealed the Krycek and Marita are lovers and working together.  Mulder and Scully go to the installation, seeking information (trying to find the Anasazi) but are stalled by the head of the facility.  Mulder sees Marita who is instructed to escort them out but takes them to the labs where she shows them black oil that she has been working on with the Anasazi who appears to be immune to it. 

While in the presence of the black oil, Mulder has an attack (severe headache) and stumbles outside where he sees Albert Hosteen.  Albert relays the story of the Medicine Wheel to Mulder -- courage, strength, wisdom and curiosity.  He says Mulder has all four of these virtues.  Scully and Mulder leave the installation just as Marita poisons everyone in the lab with a low dose of sarin nerve gas and she and the little man escape.  Later, at a motel, Mulder has trouble sleeping and starts to think about the vision of the Native American massacre he had.  He realizes that it connects to the Anasazi.  That the Anasazi has not been returned to earth as a gift, but as a trojan horse, to return the planet to its rightful owners (and that Jeremiah is working to that end). 

Krycek finds Mulder out for a run and tells him he is affected by the alien artifacts because he was 'cured' of his problems (in Biogenesis) by nanocytes, which were given to the consortium by the aliens.  He also tells Mulder that the Col. in charge of the installation is an alien (Col. Grey). 

Mulder and Scully end up back at the installation, but this time Charlie is there and makes Mulder and Marita (also there) inject themselves with the alien serum that the installation scientists under Grey were working on.  The serum doesn't affect Mulder, but Marita dies.  Charlie lets Mulder and Scully go.  Strughold tells Charlie that as a young man he worked with top Nazi scientists (Josef Menegle is alluded to). 

Back home Scully keeps watch over Mulder while she has the serum sample and Anasazi tissue samples examined. 

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Children of the Damned:  VS13x01 

Mulder's visions are back but this time, he sleepwalks in them, leading him to a variety of dangerous places and almost to the psyche ward.  Eventually, he comes to realize that the visions are a warning of what is going to happen SOON. 

He goes about trying to find others who could hold the same genetic markers as he does.  He tracks them down, in each case they are busy 'going somewhere' but when questioned none of them know where or why they are going.  They are led to a bridge (for mass immolation) but he finally gets through to them, leading all but three to safety.  From a helicopter monitoring the events, Charlie is furious that Mulder has saved his own ass and the day.  He vows revenge.

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AT LAST

Basically, around a great film noir dream of Scully's, Mulder admits that he's having dreams of Nazi scientists working on him -- experimenting on his brain.