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I would like to bring this bac towards the OP's original idea, so allow me to repost something I wrote in a Mordekaiser thread:
As for him (Mordekaiser) being a General, that may still be the case. We just have to remember that, since he IS of the Shadow Isles and his presumable boss Hecarim has shown up, he may not be getting the highlight as a "Big Bad" character anymore and instead may have been downgraded into the "Dragon"-villain archetype (for those who don't know, that being the Big Bad's right-hand enforcer).
EDIT: Just found something you might be interested in.
After capturing the West Altar in the new Twisted Treeline with Hecarim it will sometimes say "Mordekaiser is not to be trusted, Hecarim!" This seems to confirm the idea that Mordekaiser is a subordinate of Hecarim or the two merely have an alliance of some sorts, but that either way Mordekaiser is seeking to stab him in the back and, maybe, claim Hecarim's army of undead riders to add to his own army of souls!
Or, interestingly enough, Mordekaiser may be the true leader of the Shadow Isles; the East Altar in particular seems to have much reverence for him, although the East Altar also does not appear to be completely sane or good-natured any more.
On the note of the altars: Mordekaiser being a prisoner is still hinted at by the West Altar:
"Mordekaiser... Are you also a prisoner?"
Could be what Morde is looking for in his new lore is a way to free himself of his armor prison.