Upon entering the Citadel, you'll be immediately confronted with the evil villain of the story.
After a very short amount of dialogue you get into a battle with Zephyros. He's not the final boss for no reason, he's the toughest battle in the game.
He'll get bored of scratching you after a while, and then the battle will get serious. Just keep attacking with Nien and healing with Sevan.
He will not sometimes take a stance and appear covered in purple electricity. If he does, focus entirely on healing. The charged attack will do a ton of damage, and if you're not at peak health you'll likely not survive.
If someone goes down, use one of the Phoenix Downs you bought back at the town and then focus on healing. If Sevan is casting heal and Nien is using Potions you heal way more than the boss deals in that time.
No matter how hard you try though, this boss is unbeatable. If you survive long enough to see his health low, he'll just heal up. The only way to continue is to both die to him. A cutscene will then show Zephyros killing Sevan permanently.
When she dies, you obsorb her power and unlock a hidden abaility! Remember that let you transform into a Dragon? Well now you can use it! In fact, using it is the only way to deal enough damage and kill Zephyros.
If you get into a battle on the way back to town, you'll notice that the Dragon Ability really does have a long cooldown. Not months like the item said, but still not really worth waiting to use in a wild battle.
The only way you're getting to the Mana tree is by Airship, so lucky for you, Ate will lend you his when you go back to town.