He had nothing to do with Minfilia being pulled into the aetherial sea in the first place.

Elidibus came to him at the end of 2.55, after the banquet, and offered to reveal deeper truths to him. It's quite possible that Elidibus intended to recruit Urianger to the Ascians – a truly terrifying thought to have him as an adversary – but in any case Urianger was just playing along and seeing how much valuable information he could get from it.

Then through late Heavensward into 3.2, we learn of Minfilia's fate of being pulled into the aetherial sea by a weakening Hydaelyn, last known to have been struggling to hold her form together at the Antitower.

Meanwhile, because he was working with Elidibus, Urianger got assigned to assist the Warriors of Darkness, as we first see at Xelphatol. This is the "Dark" he laboured to set against (the Warrior of) Light – quite directly by suggesting Ardbert should try to kill us rather than fiddling about with primals – resulting in us bringing the six crystals together, getting everything into position without Elidibus catching on until it was too late to do anything about it.