In contrast to other games in the series, Etrian Odyssey III has three different endings based on what route you take in the game, starting from the choice required to make after entering B11F.
Armoroad Route - Porcelain Wish
This path results from choosing to side with Armoroad after encountering Kujura on B11F. Flowdia and Princess Gutrune intend to fight the Deep Ones directly, and task you with defeating the Gatekeeper in order to infiltrate the Abyssal Shrine. Once inside, you are tasked to retrieving the Amarantos flower from B15F for Gutrune's sake.
At B16F, while investigating the Abyssal King's search for the teleporter, Olympia approaches the party and summons Kirin to fight you as stratum boss. While pursuing them in the Porcelain Forest, Olympia unleashes Mortal Hunters at various point to deter the party.
Reaching the glade at B20F, the party arrives in time to stop the Abyssal King from attacking the Princess. Both the Automaton King and Olympia are fought simultaneously as the final battle of this route. With his defeat, the Abyssal King briefly regains his humanity as he dies, while the Yggdrasil Tree laments his fall.
Upon loading a Clear Save, a newly reconstructed Olympia appears as delivers a message from Yggdrasil: head to the Cyclopean Haunt and fight the evil that sleeps beneath to atone for the Abyssal King's death. She then returns to the Deep City to maintain the Celestial Palace. Turning in the final mission at Via Senatus will award you with the Armoroad Emblem, an accessory that increases HP by 100 and all stats by ten.
Deep City Route - Abyssal Desire
This path results from choosing to side with the Deep City after encountering Kujura on B11F. The Abyssal King believes mankind cannot safely fight the Deep Ones directly as they feed on emotions. He asks that you protect the Gatekeeper which prevents Deep One incursions.
Once that is no longer possible due to Kujura tricking you into killing the Gatekeeper, the King instead asks that you commune with the Yggdrasil tree in the shrine itself. Olympia provides further instructions. The Yggdrasil reveals that it crossed the "pitch-black sea" in pursuit of an ancient evil, which it sealed at the bottom of the labyrinth. It also reveals that a Deep One has infiltrated a high-ranking member of Armoroad: Princess Gutrune. The Abyssal King ultimately bestows the task of eliminating that infiltrator upon you.
Once reaching the teleportal to the Porcelain Forest, Kujura attempts to intercept you. He is halted by Olympia who was sent to cover you, but not before he summons a beast known as Shin to fight you as stratum boss. Kujura further tries to halt your progress into the forest by unleashing mantises.
Reaching the glade at B20F, the party encounters Princess Gutrune. She explains she only borrowed the Deep Ones power in hopes of eventually finding her brother. Kujura attempts to hold off the party directly but falls. In anger, Gutrune loses control over her state and transforms into the Deep Princess, which attacks the party. Upon being slain, she briefly regains her humanity and laments being unable to reunite with her brother. In the ending, a voice belonging to presumably the Abyssal God notes the plan to infiltrate Armoroad has failed, and will keep waiting millenia until the Eldest One fully awakens.
Upon loading a Clear Save, Olympia asks that you speak with the Abyssal King, who explains how to reach the final stratum where the threat below awaits. Turning in the final mission will award you with the Deep City Emblem, an accessory that increases TP by 100 and all stats by ten.
Eldest One Route - Eldest Path
This route is more complex because it requires specific steps to be completed. First, two items must be obtained during the story. If the party said "Yes" to Olympia's request to keep the Deep City a secret, after reaching B14F she presents the Starry Shard, explaining the Abyssal King no longer is able to use it on behalf of his loved one. Likewise, if the party answered truthfully about finding the Deep City to Flowdia, Kujura would eventually leave the Sky Bowl in your guild's care. To obtain both items, you must therefore agree to keep the Deep City a secret, and then break your word when reporting to the Senatus.
To fully initiate this ending router and break off the other two, once you turn in the mission to locate the teleportal after defeating Kirin/Shin, you must not start the final mission. Instead, using the Moon Key obtained after the 4th Stratum Boss, return to the Hall of Conviction on B10F and speak with the Eldest One.
He will confess to once meeting Gutrune and a deal he made with her, and if both the Starry Shard and Sky Bowl are in your possession, reveals that they are components of the Porcelain Offering. He reassembles the bowl and hands it back, but not before branding your palm. The party must now find the Abyssal King and Princess Gutrune on B20F and present the Porcelain Offering, allowing them to regain their humanity and their reunion.
After delivering the Offering, the brand reacts and delivers a request by the Eldest One to proceed to the barred door within the Abyssal Shrine on B16F. This enables access to a hidden area not available on the other routes. At the deepest chamber lies the Eldest One, who was able to restore himself to full power now that the gift he gave the Princess was returned. He then transforms into the Progenitor and faces the party in the final battle. Once he is defeated, the Eldest One explains how he came to the world along with the Abyssal God from deep space and were followed by the Yggdrasil tree. As he fades, he explains how his god still sleeps in the depths far beneath Yggdrasil.
Upon loading a Clear Save, Olympia relays a final request from the Abyssal King to venture into the depths and confront the dark god. Unlike the other ending paths, there's no final mission with a reward at the end, aside from equipment unlocked via item drops in the secret area of the Abyssal Shrine.