The Primarchs were the twenty genetically-engineered "sons" of the Emperor. Using his own DNA in their creation, the Primarchs were designed to be far superior to even Space Marines: they were taller, stronger, faster and more intelligent. They were also incredibly charismatic and were well suited to their role as the generals and leaders of the Imperium of Man.
Several of the Primarchs at the Triumph of the Ullanor Crusade. From left to right: Sanguinius, Mortarion, Magnus the Red, Angron, Jaghatai Khan, Lorgar, Rogal Dorn, Horus, and Fulgrim
Horus Lupercal being made Warmaster of the Imperium in Ullanor. From center counter-clockwise: Horus, the Emperor, Magnus, Mortarion, Lorgar, Angron, Jaghatai Khan, Rogal Dorn, Rogal Dorn's mustache, Fulgrim and Sanquinus.
The Primarchs were created in a secret underground laboratory on what used to be the Himalayas, under the tightest security. All of them were derived from a subset of the Emperor's DNA that served as a template, which was altered differently for each of the Primarchs; it is also thought that he engineered them spiritually as well using long-forgotten psychic techniques. As the Raven Guard discovered after the Emperor granted them access to the original data from the Primarchs' creation, many of the Primarchs' gene-samples were wildly divergent from the original template- some had long gene sequences deleted, while others had non-human DNA spliced into them for reasons only known to the Emperor. (A particularly intriguing discovery was one sample labeled "Subject VI", which had extensive amounts of canine DNA added to it.) However, due to insidious dickery and in spite of the safeguards the Emperor had set up, the forces of Chaos were able to spirit the Primarchs away from the laboratory and scatter them across the universe. Just as planned. Somehow, the Emperor knew his sons were still alive, but had no clue to where they could be, so he decided to go ahead with his Space Marine project. Using DNA samples from each Primarch before they were abducted, the Emperor created twenty legions of Space Marines, in what would later be called the First Founding.
Each of the young Primarchs were forced to adapt to the lifestyle on their new homeworld, something which would influence and mould them throughout their lives. The Primarchs rapidly grew to adulthood and quickly rose to power, often becoming the leaders of their world. As the Emperor crusaded to unify the galaxy he would occasionally stumble upon another long-lost son. When this happened, the Emperor would hold a celebration in honor of this discovery, give the Primarch their legion to command, then tell them to fuck off and start conquering worlds while he fapped to his favoured offspring. The Emperor was a dick like that.
The first Primarch the Emperor discovered was Horus, who would become the Emperor's favoured son. The majority of Primarchs somehow recognized the Emperor on sight, immediately pledging their allegiance to their father. A few (such as Leman Russ and Vulkan) only swore allegiance after being bested in a contest. Angron outright refused to follow the Emperor, preferring to die in battle along with his rebels in their fight against the oppressive Not-Romans. The Emperor simply shrugged and abducted his son, leaving Angron's followers to get slaughtered. Angron never really got over that dick move.
At the end of the period known as the Great Crusade, Horus, who had recently been promoted to the title of Warmaster, fell to Chaos and rebelled. It didn't take long for eight other of his fellow Primarchs to join his side against the Emperor, resulting in a full-scale civil war known as the Horus Heresy. Funnily enough, most of the Primarchs who sided with Horus were those who felt that the Emperor had taken a giant, steaming dump on them. So while the Emperor is the greatest tactician, biologist, warlord, and leader in the history of mankind, he's worse than a crack-addled transient junkie as a father.
 Primarchs and Legions
||Name of the Legion
|Alive, asleep within a secret chamber on The Rock. He will awake... someday.
||Daemon Prince of Slaanesh, ruler of the Pleasure World.
||Daemon Prince, ruler of Mendregard.
||Unknown, disappeared into the Webway while hunting Dark Eldar.
||Unknown, disappeared into the Eye of Terror but promised to return one day.
||Deceased, killed while boarding a Chaos cruiser during a Black Crusade. His remains were recovered, and his skeletal hands were placed in shrines. Rumored to still be alive.
||Deceased, assassinated by Callidus assassin. His body was never found.
||Deceased, slain by Horus. May or may not be the Sanguinor.
||Deceased, slain by Fulgrim and his head offered to Horus as a gift. Some claim he is still alive on Mars, though his is unlikely.
||Daemon Prince of Khorne.
||In stasis, technically alive. Might be getting better somehow, unfortunately.
||Daemon Prince of Nurgle, ruler of Plague Planet.
||Magnus the Red
||Daemon Prince of Tzeentch, ruler of the Planet or Sorcerers.
||Luna Wolves/Sons of Horus/Black Legion
||Deceased, slain by the Emperor.
||Daemon Prince, ruler of Sicarius.
||Dead(?)- it's a long story. Believed to return eventually.
||Missing, last seen heading for the Eye of Terror. Some believe he will return.
||They're not telling.
|| It's complicated
 It Sucks To Be Loyal
An accurate retelling of the final stages of the rebellion.
- Horus was killed by the Emperor during the Siege of Terra, who utterly destroyed his soul, and his body was destroyed by Abaddon. He is very dead, but that was his fault for being a fuckwit.
- Angron is a Daemon Prince of Khorne. Still gets shit done. But did get his arse handed to him by the Grey Knights on Armageddon.
- Mortarion is a fucktwit who rarely does anything of interest, but is a Daemon Prince of Nurgle. Got some open heart surgery, courtesy of Draigo/Ward.
- Fulgrim's soul was trapped in a painting while his body was possessed by a Daemon for a brief time before swapping places with the daemon and taking its powers (or so he claimed). Later becomes a Daemon Prince of Slaanesh.
- Lorgar is a lazy fucknut who does nothing since they fled to the eye of terror, but still a Daemon Prince of Chaos Undivided.
- Magnus the Red is... derping out, and screaming Just as planned every time something happens, but he's a Daemon Prince. He sometimes also gets shit done, leading armies to the Space Wolves' planet and screwing with the Imperium, keeping his big red trollface on all the time until he gets his ass tossed back into the warp.
- Perturabo becomes irrelevant after he goes on to drop entirely out of post-heresy fluff, but is still a Daemon Prince of Chaos Undivided. Helps Failbaddon in a couple of Black Crusades, by giving him some Daemon Engines. It doesn't really help, though.
- Konrad Curze is dead but he allowed the Callidus assassin's infiltration, apparently wanting to die after becoming the very thing he fought against.
- Alpharius / Omegon... your head will explode, so we won't bother explaining the specifics. Surely, they are making plans so intricate and troll-worthy that even Tzeentch could not comprehend all the subtleties behind them.
- Ferrus Manus was killed by Fulgrim during the Drop Site Massacre. His body was not recovered, so some Iron Hands think he might still be alive. But the fact that he was decapitated by Fulgrim after being defeated and had his head delivered to Horus makes this claim fairly dubious. Just don't say that to the Iron Hands, though. Unless you want free open-heart surgery from a ceramite and steel power fist.
- Sanguinius was killed by Horus. His body was recovered, and he's the only Primarch who doesn't have any legends about returning, though there are some theories on the identity of the Sanguinor. (For what it's worth, Fear to Tread shows that the Sanguinor is indistinguishable from Sanguinius himself and had enough power to appear in the mind of an Apothecary shortly before the Blood Angels were deployed to the Signus system.)
- Lion El'Jonson returned to Caliban only to discover
that his friend Luther had stabbed him in the back. THAT LUTHER HAD A PLANET-WIDE PARTY AND EVENTUALLY PASSED OUT INTO A COMA AFTER DRINKING 2 TANKERS OF SPACE WOLF-GRADE ALCOHOL. He sleeps deep within the Rock, on life support (but none of the Dark Angels seem to know this).
- The "life support" part just got retconned; he's fully healed and battle-ready, waiting for the Emperor to tell him to wake up.
- Jaghatai Khan disappeared into the Webway after chasing a group of Dark Eldar. The White Scars think he will return someday, and when you consider the fact that time is just as weird there as it is in the rest of the Warp, there is a small possibility he's still around.
- Leman Russ disappeared into the Eye of Terror but promised the Space Wolves that he would return for the Final Battle. Magnus appears to know where he is now, but he sure as hell isn't telling the Space Wolves. Reports during the Thirteenth Black Crusade claim that a figure matching Russs's description was seen leading the 13th Great Company have surfaced, but were never verified.
- Rogal Dorn was killed during a Black Crusade in a desperate ship boarding action. His remains were recovered and his skeletal hands were enshrined.
- Roboute Guilliman is perfectly preserved in a stasis field, seconds from death. It is rumored that he is healing, even though it is impossible for anything to change inside a stasis field. Most people credit the healing to be the power of the Emperor, which says something about the Imperium as that's considered a valid argument. It says something further about the setting in that a number of fans believe that this is a valid argument. This may be true following the Iron Heart device in Angel Exterminatus healing someone in stasis, very very slowly. Fortunately, being suspended in a stasis field ensures you feel whatever you were feeling at the instant of your immersion for the duration.
Rawbutt Girlyman was in excruciating pain, ensuring that the living embodiment of the Great Beast's nightmarish seed is, to say the very least, not a happy camper. The human body is programmed to dull pain as it dies and Astartes modification takes this to the extreme. He's probably high as a kite now. Matt Ward seeks the power to resurrect Gulliman. In his quest to do so, he created Kaldor Draigo.
- Vulkan got the shit kicked out of him during the Drop Site Massacre, and had to be dragged into a Thunderhawk in bloody tatters. He vanished under unknown circumstances some time after the Horus Heresy; the Salamanders believe that he is still alive and that collecting the nine relics he left behind will reveal his location.
The fact that the next Horus Heresy book is called Vulkan Lives makes it pretty obvious that he's alive and well. He has been confirmed dead in that book after burning alive in a teleport mishap. On the other hand the afterword hints that he may not have actually died and in fact heavily implies that he may be a Perpetual and thus is incapable of dying at all.
- Corax disappeared into the Eye of Terror as an atonement for putting down the mutant hordes he created in trying to create Space Marines out of desperation. Quoth the Raven: "Nevermore."
So most of the traitors are Daemon Princes (which, ignoring the brain-rape, fucking rules) while all of the loyalists are dead, have disappeared, or are in comas. The chapters have legends which hold that the Primarchs will return and heal the Emperor, launching a new Great Crusade. Note:
when GW says “disappeared” they actually mean “we are going to bring them back in a massive deus ex machina”. No they don't. They're not Blizzard. But since that would require advancing the plot, it's not going to happen any time soon.
 Two Missing Primarchs
Who are the two missing Primarchs, you ask? Sigmar and Archaon (depending on how WHFB fits in with 40K, if it does). Or maybe (per /tg/ canon) Rachnus Rageous and Tialoc Ekans. Samus and Guts are also contenders.
Okay, fine. Nobody really knows. What has been established is that they got killed for some reason and the existence of their Legions was wiped from record by the Emperor. The surviving marines from their Legions were then allegedly gobbled up by the Ultramarines, for some retarded reason. Curse you, Smurfs.
Games Workshop have mentioned Primarchs besides the eighteen above on other occasions, but they backtracked since. Back in the first edition of Warhammer 40,000, all twenty First Founding Chapters were known, as were their Primarchs (though, at the time, the Primarch was just the first Chapter Master). Of these, the Valedictors and Rainbow Warriors were declared in a later White Dwarf to have been founded after the Second Founding.
Later, in the short story Hell in a Bottle from the novel Into the Maelstrom, a chapter known as the Iron Hearts get fucked over by a Chaos Lord. The short story also mentions that the Chapter has a Primarch known as Rubinek. Of course, this was just a huge cock-up on the author's part, who himself admitted that he meant Chapter Master.
The Horus Heresy novels fill in some of the blanks, but they still leave a lot of questions open. In The Lightning Tower Rogal Dorn says that the lost Primarchs' disappearances were "separate tragedies", so it seems like they disappered in two different incidents. Deliverance Lost suggests that whatever happened to the missing Primarchs occured sometime before the Emperor found Corvus Corax, as Corax asked the Emperor why there were only sixteen other Primarchs waiting for him if he was the nineteenth found; the Emperor avoided the question, claiming that "it would be a discussion for another day". The First Heretic specifies that the missing Legions were purged at least 43 years before the Drop Site Massacre, so we can conclude that neither one took part in the Horus Heresy. At the same time, members of the Word Bearers Seventh Company travelling through time with Ingethel the Ascended reveal rumors that the surviving members of the lost Legions were folded into the Ultramarines (their Chaplain thinks the rumor is a load of grox-shit, but their Captain does note that the Ultramarines are on record as receiving an increase in troops). Finally, it also adds that the remaining Primarchs had to swear an oath never to speak of their missing brothers and that the missing Primarchs' corresponding legions were personally purged by the Emperor, so it had to have been something extraordinarily bad. Leman Russ mentions in Prospero Burns that the Space Wolves had fought other Space Marines before the attack on Prospero, which may have something to do with the purge. Several books since have backed this up. Gene-seed flaws might have played a major part- in Fear To Tread, Sanguinius admits to Horus that he had not told the Emperor about the Red Thirst because he feared that the Emperor would purge the Blood Angels in the same way as the missing Legions.
Out of universe, Rick Priestley admitted that the unknown legions were supposed to be a reference to the three Roman legions wiped out in the Battle of the Teutoburg Forest, whose numbers were never reused after they slain to a man by German barbarians (as well as a way to let fans design their own Legions to fill in the gaps for themselves). Clearly he didn't think out the implications that this would have on the setting.
 Rules on the Tabletop
Thanks to Forgeworld, not only do we have models for the Primarchs, but rules as well. As you can guess, they are ungodly rape machines who can easilly win their points back and more. That's not to say they're invincible, though- they can still be killed if you screw up badly enough.
Konrad Curze/Night Haunter
Alpharius and Omegon... maybe