"Hmph. So, It begins. I suppose it’s time to do something inexplicable.... again.”[1]
Cypher' is the leader of the Fallen Angels. His true allegiance is unknown, as he is just as likely to help Chaos-aligned forces as he is to assist Imperials. He has constantly evaded capture by the Dark Angels for Millenia.
Official Canon
The original Lord Cypher was a title inherited from one of the rival Knight Orders that Lion El'Jonson fought against, prior to his reunion with the Dark Angels. The last surviving member was made part of the legion, and knew of the existence of Chaos. While he did tell Luther about Chaos, what his plans were during Luther's rebellion was unknown. He was supposedly killed, and his title was given to Zahariel.
After that, it's unknown what became of Cypher, whether it's the same individual or a title passed between Fallen. He may in fact be a time traveler who was responsible for scattering the Fallen in the first place, as he was able to unite several artifacts in the 40th millenium that brought him, Azrael, and Typhus back in time to witness the fall of Caliban.
The sword on his back is likewise mysterious, as it is never seen unsheathed. Some speculation is that its the Lion's own sword.
TTS Canon
Cypher decided it was time to do something "inexplicable"[1] and lead the Adeptus Mechanicus to a planet in the Orior sector where giant ancient speakers were found.[2] Satisfied that this would make the planet "rival Terra itself in its sacredness,"[3] he snuck aboard the Dark Angels' ship as they arrived to investigate Cypher's activities. Azrael himself mistook Cypher for another Dark Angel.[4]
Cypher, along with the rest of the Dark Angels, are traveling on their way to Mars. Eldrad Ulthran revealed that he was in league with Cypher, and should the plan to summon Ynnead go awry, he would need Cypher and Sylandri Veilwalker to find and recruit a certain "big bewildering bag of hooded dicks," presumably Belisarius Cawl.[5]