Ezequiel knew Eligos and the other two Mind Rulers would unleash a devastating soul invasion spell as soon as he showed up. Although his Lord of Emptiness Bloodline and his True Will granted him spiritual defenses shockingly high, he was not so arrogant as to look down on a Primarch known as a master of soul invasion spells.
That is why Ezequiel first generated a clone composed of 5% of his cells, whose soul aura was indistinguishable from the real one, making it so that the three Rank 9 Mind Rulers would unleash their mighties soul strike against this one.
Ezequiel's plan worked. Now there was no more energy left in that tower, and the lightning storm cut any connection to the outside, so Eligos and the other two would have to face him on their own.