The tower dungeon's layout is similar to Via Infinito. It has 80 levels in total, and at every 20th level, the player has to fight a boss. On every tenth level, Yuna, Rikku and Paine will have a conversation about what has happened since the events in Final Fantasy X-2.
Three months after the events of Final Fantasy X-2, the members of the Gullwings have gone their separate ways: Yuna is living with Tidus in Besaid, Rikku is working mission after mission, and Paine is wandering Spira by herself. They are brought back together after each received a letter that called them to explore the newly discovered Yadonoki Tower as a group.
As the trio explores the tower ruins, they converse over what they'd been doing since they had separated, and why they hadn't stayed in contact. The conversation escalates as Rikku expresses her jealousy towards Yuna who had reached her goal in life and settled down. The bickering between the pair causes Paine to raise her voice against them. Eventually, Paine reveals the sender of the letters was herself; citing it was her wish to not lose the friendship that they once shared, having learned from both her previous friendship with Nooj, Gippal, and Baralai, and from her own lonely travels.
On the final floor the trio encounters Major Numerus, who appears to be sealed or "shut down" prior the disturbing of it's slumber. Before attacking the party "CAUTION", "KEEP OUT" and the following verse (a possible reference to the "spiral of death"):
- each new death holds
- the promise of life
- each new life brings
- the promise of death
- the circle is unbroken
in Spiran letters can be read on his body. Major Numerus has to be defeated three times before the final stair can be climbed.
The trio travels to the top of the tower where they find a broken machina, whose upper part slightly resembles Sin, and not much else. However, due to their conversations, they realize the machina is a bit like their group: broken and separated. As they vow to be more than just strangers who met by chance, becoming friends once again, the machina begins to work, and their adventures continue...
The themes that play during the player's trek within Yadonoki Tower are called "Last Mission No.1", "Last Mission No.2" and "Last Mission No.3". The tracks appear in the Final Fantasy X-2 International + Last Mission Original Soundtrack as tracks 4, 5 and 6 respectively.
- If the file used during the Last Mission playthrough is 100% file, an unlockable video will become viewable through the main menu.
- Moving and battling in the tower is done differently from the rest of the game. Everything is turn-based, similar to Chocobo's Mysterious Dungeon. Fiends appear on the map, the player chooses their action (which can be moving, changing Dresspheres etc.), then the fiends will take an action. Finding an elevator will allow the player to advance to the next floor.
- Yadonoki Tower's location in Spira is never revealed.
- Not a single symbol associated with Yevon is found in the tower, making it possibly older than Zanarkand and Bevelle.
- The name is an Al Bhed translation of maboroshi, meaning phantasm or illusion. A series of promotional collector's cards uses the English-Al Bhed name "Abrasanym Tower", or Ephemeral Tower.