Two unknown legions
Precious little is known about two of the twenty Space Marine Legions, numbered II and XI, and their respective Primarchs, as their records are simply noted as having been "expunged" or "destroyed" in Imperial listings of the 20 Legions.
However, nothing is known for sure about the names of the legions, their Primarchs, homeworlds and their ultimate fate. There are conflicting reports as to whether the two unknown Legions met their fate prior to or after the Horus Heresy and which side they joined in the Heresy if they participated in it.
Currently, all that is stated about this issue is:
- The Emperor created 20 Primarchs, who were snatched from Terra by a Chaos vortex and scattered around the galaxy.
- The 20 incubation capsules drifted through the warp for decades or even centuries, until finally coming to rest on human-inhabited worlds throughout the galaxy, "where they were variously adopted by human parents."
- The only exception to this is the Primarch Konrad Curze, who survived utterly alone (and whose background, in any case, was only described in later material).
- In the listings of the 20 Legions in Imperial records, Legions II and XI are stated as having "all records expunged from the library". Earlier background (Codex Imperialis and second edition's Ultramarines codex) less ambivalently states that the records for these two Legions were deleted following the Heresy. Considering that the Traitor Legions are simply listed as excommunicate traitoris but still included in these same lists would mean that the records were deleted deliberately and for a reason only known by those who perpetrated the action.
- Of the various abilities possessed by the Primarchs, one was "invisibility".
- If this is taken literally, this presumably refers to one of the missing Primarchs, as invisibility is not a power possessed by those known. It could also mean this Primarch was a blank as such individuals are said to be invisible to psykers.
- This could also be referring to Corax who is said to have effective invisibility, whereby he could walk among people without them noticing him. It is also said that only the Emperor knew this about the primarch.
- The Emperor met each Primarch in turn, and each Primarch had risen to a position of authority within the cultures they had found themselves in.
- 20 Legions took part in the Great Crusade, each led by their own Primarch.
- Alpharius was known to be the last Primarch to be found, a fact which even earned him the nickname "The Last". This suggests that all the other Primarchs had been found already.
- 20 statues of the Primarchs were erected in the Imperial Palace on Terra. By the time of the Horus Heresy, plinths II and XI "...had been vacant for a long time. No-one ever spoke of those two absent brothers [and] their separate tragedies."
- This suggests that the two unknown Primarchs had been found previously and that something tragic had happened. The two Primarchs were "absent" but not referred as "dead".
- All Primarchs were tempted by Chaos and "fully half" of them failed that test.
- This suggests that possibly 10 Primarchs were, in some way, corrupted by Chaos influences. The known traitors are nine (Fulgrim, Perturabo, Konrad Curze, Angron, Mortarion, Magnus, Horus, Lorgar, and Alpharius). Whether an additional Primarch was corrupted or not is unclear.
- Prior to sending Sigismund and his Imperial Fists to Mars during the Heresy, Dorn muses to Malcador on the loyalist support of two legions, possibly the two unknown legions, during the Heresy. Malcador quells the Primarch's thoughts, stating that "They are lost to us forever."
- Horus convinced "no less than 9" Space Marine Legions to side with him at the onset of the Heresy, a number also referred to as "fully half" of the legions. When he assaulted Terra, this number was given as 9.
- This also implies, but does not categorically state, that the 9 known traitor legions are all of the legions that followed him into rebellion and that 18 legions were the total number of legions active at the time. A passage detailing Horus' plans for the various legions at the outset of the Heresy mentions by name all 18 known legions.
- "Of the original 20 Primarchs only 9 survived the Horus Heresy. The remainder were either killed in the fighting (like Horus) or fled with their [Legions] into the Eye of Terror. The survivors helped [to rebuild] the Imperium."
- It is currently accepted that 3 Primarchs died during the Heresy (Ferrus Manus, Sanguinius, and Horus) and 6 are known to have fled into the Eye of Terror (Fulgrim, Perturabo, Angron, Mortarion, Magnus, and Lorgar). The fates of the other 11 are open to multiple interpretations. However it is commonly believed that Roboute Guilliman is in stasis as his throat was cut and Lion El Johnson's body has been hidden away in the belief that he shall return one day.
- Two traitors, Konrad Curze and Alpharius, did not flee into the Eye of Terror and were killed later on. 7 loyal Primarchs seem to have survived. It is possible that Curze and Alpharius were counted as part of the 9 survivors. However, in the novel Betrayer it mentions the "18 Legions", a clear statement that the unknown legions disappeared before the Heresy, and played no part in them.
Second edition's Ultramarines codex states that it seems likely that Legions II and XI fought for Horus at least during the beginning of the Heresy. It also refers to the records as being destroyed following the Heresy. However this conflicts with more recent information in the novel The First Heretic where Magnus and Lorgar discuss the two unknown primarchs and the death of them and their Legions 43 years before the Drop Site Massacre. 
The short-story Hell in a Bottle by Simon Jowet mentions a Primarch Rubinek of the Iron Hearts chapter. Primarch Rubineck is not mentioned anywhere else. Some authors seem to occasionally confuse the Chapter Masters with the Primarchs and Rubinek was most likely such a case.
As Horus lay in coma inside the Davinite temple after being wounded by Eugen Temba, Erebus gave him visions that showed him events from various points in time. In one of these experiences, Horus found himself in the geno-vault where he was created, and looked down upon the genetor-tanks containing the infant Primarchs. At one point he stops before tank XI and reflects upon the "untapped glories that lay within, knowing they would never come to pass". This refers to one of the unknown Primarchs. Later on, Horus' anger takes control and he smashes his fist upon tank XI, damaging it. Shortly after, a vortex swoops up all the genetor-tanks and scatters them across the galaxy.
The truth of this vision is unclear; it should be noted that the whole experience was orchestrated by the Chaos powers, in other words Horus saw what the chaos gods wanted him to see.
When Dante asks the Blood Angels' successor chapters for men to bring the Blood Angels back to full strength, having suffered heavy casualties during Arkio's heresy, Seth, chapter master of the Flesh Tearers, makes a counter to this demand: disband the Blood Angels and spread them amongst the successors. When Orloc (chapter master of the Blood Drinkers) protests that there is no way a First Founding Chapter can end like this, Seth retorts that, actually, it has happened before. 
This statement is no definite indicator, as the two Unknown Legions were legions and not chapters. Additionally James Swallow is known for taking certain liberties with the way he depicts the Blood Angels. Technically there are no first founding chapters, as chapters did not come into existence before the second founding (which Swallow might be referring to as "first").
A Crimson Fist
In the short story A Crimson Fist, Sigisumund looks at the shrouded statues of the Traitor Primarchs, and says that they are traitors and should be torn down. This could be a hint saying that the two missing statues were torn down because the unknown Primarch(s) were traitors as well. But using information from Betrayer, this would mean they were traitorous before the Heresy.
The First Heretic
The First Heretic (Novel) sheds more light on the subject of the two unknown Primarchs:
- The Lost Primarchs were erased from Imperial records at least 43 years prior to the events of Isstvan V, as only eighteen Legions are referenced during the events at Monarchia. This could be a precursor to the Horus Heresy, the belligerents serving the chaos gods. However, this seems unlikely as the primarchs would be aware of chaos, yet are easily seduced by it.
- It is implied that the Emperor personally cast aside the two lost Primarchs: "I fear the Emperor will break the Word Bearers - and break me. We would be cast alongside the brothers we no longer speak of."[18b]
- Throughout the remainder of the Great Crusade, the remaining Primarchs swore an oath not to even talk about the lost Primarchs.[18b]
- The lost Primarchs/Legions are referred to as 'the forgotten and the purged'. This could simply be a way of describing traitors, or they are references to the individual legions (i.e.-one legion "the forgotten" and the other "the purged")[18b]
- Magnus the Red confirms that the Emperor personally purged the two lost Primarchs/Legions from history.[18b]
- During the vision of the Gal Vorbak, the eleventh Primarch is referenced as still being innocent and pure prior to the scattering of the Primarchs. This implies that the eleventh Primarch either becomes corrupted or is guilty of some degree of transgression against the Emperor/Imperium, or both. One of the Gal Vorbak also says that killing the eleventh Primarch in the past would, "save them a lot of trouble", which could be interpreted as saying the Word Bearers had some connection with "dealing" with the legion.[18c]
- Both lost Legions are said to have been expunged from Imperial records for 'good reason'. They are said to have in some way acted shamefully.[18d]
- A rumour is revealed that could explain what ultimately became of the II and XI Legions. Around the time that the II and XI Legions were expunged from Imperial records, the Ultramarines Legion swelled in Astartes numbers to eclipse all other Legions. It could merely be a rumour, or it could actually be the case that the II and XI Legion's Astartes were inducted into the XIII Legion after they were officially expunged from Imperial records. If this were true, it would suggest that the legionnaires of the II and/or the XI haven't committed any offence; the crime lies with the primarch, and possibly a minority of the legion. This rumour however still doesn't explain what actually happened to the II and XI Primarchs.[18d]
- In the novel Prospero Burns, on an assault run into a new war zone, a group of Space Wolves were growling over the announcement of Horus as Warmaster. When asked if they were angry over the announcement, and whether they thought that Leman Russ should have been given leadership, the Rune Priest, leading the pack, said that they were really just angry that they could not be present for the announcement, since this was the last time the Emperor would fight with his Legions. He went on to explain that all the Primarchs, and their legions, were created with a purpose or "Wyrd". One was destined to be the Emperor's statesman, one to be his storm trooper, one to lead his armies, and so on. Horus was always destined to be Warmaster, the priest said. When the Rune Priest was asked what Leman Russ's wyrd was, the priest stated simply "He is the Emperor's executioner". This gives the reason why it was the Space Wolves that were sent to destroy the Thousand Sons.
- In a conversation, near the end of the novel, Leman Russ discussed the coming destruction of the Thousand Sons legion. When asked if he was concerned over the fact that Space Marines were fighting other Space Marines, he commented that this was not the first time the Wolves had been called on to perform this task. This might be a reference to the possible destruction of the Legion II and/or XI. However, Leman Russ could be referring to when he and his legion battled the World Eaters during the Great Crusade, or when he fought against Lion 'el Johnson and the Dark Angels.
- All of these events happen just prior to Horus openly turning against the Emperor. This seems to corroborate that both the II and XI legions had been destroyed or expunged prior to the start of the Horus Heresy, and as such, neither one of these legions took part in the events of the heresy itself.
- Kasper Hawser, during his narrative in the 13th chapter of the book, states: "The fortress homes of the All-father's eighteen Legions Astartes are the most formidable and impregnable sites in the new Imperium." This appears to clearly indicate that the missing legions were gone prior to the Burning of Prospero, thus prior to the Horus Heresy.
In the novel Deliverance Lost, in Corax's reflection on his first meeting with with the Emperor, the Emperor mentions that there are seventeen other Primarchs. When Corax asks how this can be possible, as he is the nineteenth, the Emperor's face becomes "bleak, filled with deep sorrow", and he says that it is "... a conversation for another day." This indicates that the II and XI Legions were already lost, and possibly expunged, by the time that Corax was reunited with the Emperor. It also suggests that they were lost in the earlier years of the Crusade, as the Emperor mentions that most of the other Primarchs had already been discovered by the time that he came to Lycaeus.
The Outcast Dead
In the novel The Outcast Dead, Evander Gregoras, the Master of the Cryptaesthesians, states that the "Wolves will be loosed again", this time to make an example of Magnus who used forbidden powers to contact the Emperor. Assuming that the Space Wolves are meant, this implies that there are people apart from the Emperor and the Primarchs who are aware of what had happened and confirms the role of the Space Wolves as an instrument to sanction other legions and Primarchs.
A Thousand Sons
Fear to Tread
In the prologue of Fear to Tread, Sanguinius is called to deal with one of his Blood Angels, Alatros, who has succumbed to the Red Thirst. Horus witnesses his brother kill Alatros and asks why he did it. The Angel initially refuses to answer, but then reveals the existence of the Red Thirst, a flaw in the Blood Angels gene-seed that turns his legionnaires into mindless, bloodthirsty killers, kept secret from his entire legion save a select few. When Horus asks Sanguinius why he never talked about that with his Primarch brothers and, above all, why he never asked for help from their creator, the Emperor, Sanguinius replies he feared the most radical solution his father could propose:
This response implies that the legions were purged because of an inherent flaw in their gene-seed and Sanguinius fears the same fate.
The Horus Heresy Book One - Betrayal
In the Forge World book The Horus Heresy Book One - Betrayal, the Primarchs and their Legions are listed in a table with the names of the II and XI Legions and Primarchs blacked out only as far as the text concealed. The length of these black lines indicates that the name of the II Legion is quite long, only just shorter than "Emperor's Children" and the name of the XI Legion is about the same length as "Thousand Sons". The name of the II Primarch is approximately as long as "Alpharius" (also suggesting just a single name) and the name of the XI Primarch is about the same length as "Magnus the Red" (suggesting either two names or one with a title). The book also states that "Of these twenty Legions, steadily expanding in numbers over time, eighteen would survive to grow into vast forces by the end of the Great Crusade - as to those that did not, nothing can be said in this record."
Also on the inside cover there is a Galactic Map of the Great Crusade era Imperium. All the important planets, Calth, Terra, Fenris, Prospero, Baal, Inwit, Hellion, etc... are listed. Every known Primarch homeworld is shown in its respected location. However in the Segmentum Pacificus there's a spot known as the "Finding of the Lost Son". This could be a reference of Alpharius as he was the last to be found and his homeworld never reveled, or it could reference where one of the lost Primarchs were originally found.
During the course of the audio-drama The Sigillite, Malcador and his covert agent Caleb travel to the deepest dungeons of the Emperor's Palace. They pass through the many halls of Malcador's collection, including the original suit of Power armor and bolter, a set of armor from the 11th Century Christian Crusades, a copy of the original Bible in Latin, the Rosetta Stone, the Huygen Probes that originally landed on Titan in M2, and hundreds of thousands of others. At one point they pass a massive door and Malcador stopped to dwell a moment. He told Caleb that beyond the door was the original Primarch lab from before a separate location was built. Caleb approached the door and noticed it was covered in symbols, many of them he recognized; an angel, a wolf's head, a snake, etc. Then Caleb noticed 'it looked like two of the symbols had been scratched out, or had worn away.' When pressed for answers, Malcador simply states that no one went in that room anymore, and walked away.
Descent of Angels
When Brother-Librarian Israfael tells initiate Zahariel El'Zurias the history of Old Night, he says that Lion El'Jonson has nineteen brothers. Since Descent of Angels takes place around the discovery of Caliban and the Lion, this indicates that the unknown primarchs were not removed from Imperial records before this time.
The Horus Heresy Book Two - Massacre
A timeline in The Horus Heresy Book Two - Massacre lists two events as <ALL DATA REDACTED>, with the Space Wolves Legion listed as taking part, in 965 and 969.M30. These could be the destruction of the two unknown legions at the hands of the Wolves.
However, the dialogue between Lorgar and Magnus in Chapter 10 of The First Heretic, which takes place no more than seven months after the razing of Monarchia (listed in that timeline at 964.M30), infers that the unknown legions had been stricken from the records for some time. If both sources are correct, this would infer that the legions were still active in some fashion before the Wolves destroyed them.
In a dialogue between the Primarch Vulkan and his equery Artellus Numeon on Kharaatan during the Great Crusade, the Drakelord confesses to the Captain that he has seen darkness in the heart of his fellow Primarch Konrad Curze. At a direct question of Numeon asking if it was not wise to discuss the matter with Horus or Rogal Dorn, Vulkan replies:
This response implies that the legions were sanctioned and purged for some reason.
The Horus Heresy Book Three - Extermination
In the creation history of the Alpha Legion, some names were REDACTED 3 times. One suggest us about the failed Legion created from the source of potentially tainted population. Other suggest the Emperor had wipe them as a failed experiment, and dont pass the proto legion state (the time when the Legion grows from the 1000-2000 proto marines and expand to a full grow legion of tens of thousands). And other suggest that like the XX legion, one of the destroyed legions have something to do with the Legion Custodes experiment and the Labrik Polaris incident. 
- 1: Index Astartes I, "Rites of Initiation"
- 2: Index Astartes II, [Needs Citation]
- 3: Index Astartes IV, [Needs Citation]
- 4: Codex: Angels of Death, [Needs Citation]
- 5: Codex: Chaos, [Needs Citation]
- 6: Codex: Eye of Terror, [Needs Citation]
- 7: Codex Imperialis, [Needs Citation]
- 8: Codex: Ultramarines (2nd Edition), pg. 7
- 9: Horus Heresy Chapbook (Anthology), [Needs Citation]
- 10: Realms of Chaos: Slaves to Darkness, [Needs Citation]
- 11: Horus Heresy: Visions of War, [Needs Citation]
- 12: Hell in a Bottle by Simon Jowett
- 13: Malleus, [Needs Citation]
- 14: False Gods (Novel), [Needs Citation]
- 15: Mechanicum (Novel), [Needs Citation]
- 16: Red Fury (Novel) by James Swallow, Chapter Seven
- 17: Raven's Flight (Audio Book)
- 18: The First Heretic (Novel) by Aaron Dembski-Bowden
- 19: Prospero Burns (Novel), [Needs Citation]
- 20: Deliverance Lost (Novel), [Needs Citation], pgs. 247-248.
- 21: The Outcast Dead (Novel), Chapter 9
- 22: A Thousand Sons (Novel), Chapter 15
- 23: Fear to Tread (Novel), Introduction / Preamble
- 24: The Horus Heresy Book One - Betrayal, pg. 29
- 25: The Sigillite
- 26: Descent of Angels Chapter 14
- 27: The Horus Heresy Book Two - Massacre pg. 19
- 28: Vulkan Lives Chapter 10, pg. 163
- 29: The Horus Heresy Book Three - Extermination, pg. 79-80