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What are some of your favorite fan theories on the subject? What do you think happened to the Second Legion?

if you scroll on down this section of the forum you will find a huge amount of discussion on the subject.

Here you go

HH3: Extermination talks a lot about [REDACTED] when it discusses the names and origins of the Alpha Legion. It explains that [REDACTED] was an experiment recruited from "potentially tainted sources". The experiment was a disaster and never passed its Alpha tests, after which it was ruthlessly destroyed by the Emperor. It also says that this [REDACTED] experiment long had been the subject of dark rumour, indicating that at least the existence of [REDACTED] must have been common knowledge at the time. [REDACTED] almost certainly refers to one of the two missing Legions.
The other missing Legion must have participated in the Great Crusade for some time, but it was already purged before the start of the Heresy. It is heavily implied the Space Wolves are responsible for this.

As to what happened to that Legion? No idea. Simply too little information to go on. I don't think it turned to Chaos (as the other Primarchs are not shown to be aware of Chaos before the Heresy). It must have committed an incredibly grave sin, one worse than the sins of the Night Lords or World Eaters during the Great Crusade, a sin even worse than the treason of Horus. After all, even the Sons of Horus and Word Bearers were not purged from Imperial records in the same way these missing Legions were.

 Iron_Captain wrote:
HH3: Extermination talks a lot about [REDACTED] when it discusses the names and origins of the Alpha Legion. It explains that [REDACTED] was an experiment recruited from "potentially tainted sources". The experiment was a disaster and never passed its Alpha tests, after which it was ruthlessly destroyed by the Emperor. It also says that this [REDACTED] experiment long had been the subject of dark rumour, indicating that at least the existence of [REDACTED] must have been common knowledge at the time. [REDACTED] almost certainly refers to one of the two missing Legions.
The other missing Legion must have participated in the Great Crusade for some time, but it was already purged before the start of the Heresy. It is heavily implied the Space Wolves are responsible for this.

As to what happened to that Legion? No idea. Simply too little information to go on. I don't think it turned to Chaos (as the other Primarchs are not shown to be aware of Chaos before the Heresy). It must have committed an incredibly grave sin, one worse than the sins of the Night Lords or World Eaters during the Great Crusade, a sin even worse than the treason of Horus. After all, even the Sons of Horus and Word Bearers were not purged from Imperial records in the same way these missing Legions were.

But being purged, iirc, was actually what happened for atoning. Their misdeeds were struck from Imperial records.

Collectively 2 & 11 are/were known to their brothers as "the lost" and "the damned".

From tidbits we can pick up in the various books there was some horrible issue with both.

My personal opinion is thus:

The Lost likely never made it to adulthood; some accident or the local culture killed him before the Emperor could get there and find him.

The Damned is more likely to be the one discussed in the early HH books; probably tried to pull something similar to the heresy, but without chaos gods, or getting any backing from any of his brothers. It was certainly just a little "I am taking my legion and starting my own imperium, with blackjack. And hookers." and then Emps told russ to go kill him and destroy the legion.

The other strong possibility is that the lost are the damned up above; and the damned just suffered from some truly horrible mutations.

 Iron_Captain wrote:

As to what happened to that Legion? No idea. Simply too little information to go on. I don't think it turned to Chaos (as the other Primarchs are not shown to be aware of Chaos before the Heresy). It must have committed an incredibly grave sin, one worse than the sins of the Night Lords or World Eaters during the Great Crusade, a sin even worse than the treason of Horus. After all, even the Sons of Horus and Word Bearers were not purged from Imperial records in the same way these missing Legions were.

This is a misconception, I think. Horus and the traitor legions weren't purged from Imperial records because what they did was TOO BIG TO BE ERASED. They ended the Great Crusade, turned the Emperor into a vegetable, ushered in a new age of Chaos, and were still out there plotting to bring down the Imperium afterwards. The 2nd and 11th Legions did none of those things, and actually ceased to exist after whatever happened to them happened. It was POSSIBLE to wipe their records, and wouldn't result in the Imperium being blindsided by some terrible enemy later. Don't forget though, that actual knowledge of the Traitor Legions is still classified and the average Imperial citizen only knows Horus as a sort of antichrist figure.

So the idea that the lost legions must have done something SO MUCH WORSE than the traitor legions is a misconception. I'm not sure if that would even be possible.

I think, something happened on Molech with one of the two lost primarchs.....
Some theory, I`ve read about somewhere.

Considering the 2 primarchs that seem to be the most effected by them being Lorgar and Magnus. I generally assume one of them stuck to the old gods or maybe considered the emperor and the chaos gods as all being gods (if this happened before he took control of his legion it would explain why the Ultramarines received a boost in #s) probably the lost. As the primarch would of been killed and his existing legion was "lost" in order to cover it up.
And the other was too entrenched in psychics which could of helped give mortarion and russ a negative bias on psychics