Well, Hydaelyn does assist us in first weakening Ultima Weapon so we can actually scratch the damn thing and then works on pulling each primal out one by one. She used all of her power to shield us from Ultima (imagine if BLM's had that spell), and was pretty weak afterwards.

When Lahabrea says: "Van Belsar, your enemy's shield is broken. The rest I leave to you."
Skip over that next line: "Come Adventurer, let's see who is mightier." This was a fight of pure strength against a Machination, but Lahabrea still was working behind the scenes.

Now during our fight with Lahabrea (needs to be harder) we see Hydalyn assisting us once again, but I think it was only once and whatever power she had left drag both Lahabrea and ourselves into the realm and that was just an epic scene. So, my guess is indeed the Mother Crystal is drained of strength and I think 3.0's story will see us trying to fight off Zodiark based on all lore until now.