Originally Posted by Summoner
I didn't understand that, either. I think it had something to do with the rain, though. The way he was acting up.....I was thinking that something was in the rain that refilled that case or something. Maybe a remnant of the Jenova Cells or something. Either that or there was still a little left. I'm thinking that maybe Cloud's GeoStigma disappearing, or the rain coming, had something to do with it. This next theory is a long shot, but here goes nothing.
SPOILERS
Maybe, since Mother was Aerith/Aeris, if I understood that correctly, and Kadaj felt such a strong need to please Mother, the rain that she caused made him kind of believe that he was with her. He said to Cloud that he was "with her at last", so that's what I'm guessing. Somewhere during the rain-scene, he became "reunited" with Mother, and believes it so strongly that he, in a way, replaced water that had gotten in the box with the cells. Besides, he's a remnant of Sephiroth. And if Sephiorth can create a Dark LifeStream, maybe Kadaj could create something like Jenova Cells.