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I know this probably didn't happen

...but the AL seem to have mastered the technique of soul transfer per PoD, pulling a soul-switcheroo in that novel

If they could transfer an AL soul to a xenos subject (a sedated captive, for example), could they not have an AL specialist cadre play an Ork boss and his nobs?

That way, the AL could manipulate the Orks at Chondax even more effectively

Kinda crazy...but I feel the AL are pretty crazy with the lengths they'd go to in order to manipulate other factions

This was never mentioned in Malevolence, but the in-universe writer would have limited knowledge.

Maybe a bit too out there?

Other ideas include Avatar-like essence transfer into a customised Ork host body and/or remote mental influence (not outright domination) by AL librarians.

Keep in mind that the soul swapping happened because Alpharius shared his blood with someone from his gene-line, it wasn't as if took some rando and popped inside of them. As good as AL are good at subterfuge, they still retain (like most Traitor Legions) a healthy dose of xenophobia and disgust towards alien species. They would likely not stoop to the level of transferring their soul to a xenos body, and it definitely wouldn't work the way Alpharius did it in PoD. At best, they could try to overwrite their minds psychically, but for guys like Orks it would be a lot easier just to rile up the hornet's nest and bait them into targets they want rather than directly controlling the WAAAGH! given the inherent risks and unpredictability of Orks in general. It's also highly possible that other boyz/Nobz would be able to tell something is off given their gestalt psychic nature that allows them to notice Genestealer infestations.