In Etrian Odyssey, you arrive as one of the many novices wanting to take a stab at exploring Etria's mysterious labyrinth. However, you soon realize that no guilds are willing to recruit novices, and you're prompted to create your own guild. As you explore the labyrinth, you meet with Etria's subaltern, Quinn, who gives you your first mission: map out the first floor of the Emerald Grove. You and your team do so, and your guild is given permission to explore the labyrinth by Etria's governing body, the Radha.
As you begin your explorations, you run into two female adventurers, a Ronin named Ren and the Hexer Tlatchga, both of whom work for Radha. After reaching the fifth floor, you're tasked by the Radha to defeat the monster impeding progress into the next stratum, a monstrous wolf called Fenrir. Once you defeat it, you are then allowed to continue your descent into the second stratum, the Primitive Jungle.
Continuing your exploration and work for the Radha, you are eventually tasked to retrieve a Wyvern Egg in order to continue the research of the monsters in the Labyrinth. Finding the nest, you head back up to town. After doing so, you are allowed to reach the 10th floor, where the Radha tasks you with defeating the guardian monster of the Jungle: Cernunnos. After hunting down and battling the beast, you finally re-open the path to the third stratum, which had been sealed for quite some time due to Cernunnos. Pushing past the seal, you reach the Azure Rainforest.
Exploring the exotic new area, you find and defeat an Ant Queen, among other challenges. Eventually you run into Ren, who is alone. She asks why you explore the Labyrinth, then warns you of the dangers ahead. Before she leaves she hands you an Old Scroll, which allows you to recruit Ronin. Going further downwards, you catch a glimpse of what seems to be a humanoid silhouette in the depths of the forest. You are fully aware that your guild is the first to reach as deep as you have, and no humans should be this far down...
You decide to report this to Radha Hall, where you finally meet Etria's Chieftain, Visil. He tasks your team with further investigation of this figure to determine whether it poses a threat to other explorers. You agree, curious yourself at who, or what, you saw. You continue your exploration of the stratum and eventually reach the end, where you are stopped by a odd young girl with red eyes and a strange, plant-like appearance. She demands to know why Men are trespassing in the Labyrinth. Have no good answer to give, she sends a Guardian of her people to attack you: the large Cotrangl, a large manta-ray-like entity. Upon defeating the Guardian, the girl flees. You follow her into the next stratum, the Sandy Barrens.
Searching the entire 16th floor, you run into the Hexer, Tlatchga, who expresses some concern over her partner, Ren. She then hands you a Hex Bell before leaving, allowing you to recruit Hexers to your cause. You continue to search the floor and find a strange wall that has a recess for a tablet inside. Having no other leads and nothing to place inside the hole, you head back to town to consult the Radha of your predicament. You are given a tablet and orders to exterminate the new beings, now dubbed the Forest Folk, as their mere existence poses a substantial risk to other adventurers. You accept, however unwillingly, noting Quinn's hesitation at following Chieftain Visil's orders... and just out of earshot, the Chieftain muses about how whether you die or succeed, a problem with the Labyrinth is solved.
Returning to your explorations, you eventually reach the stronghold of the Forest Folk. You are stopped by Ren and Tlatchga, who tell you to remember your duty to the Radha. They give you a strange look as you walk away to begin your war on the Forest Folk. Slaughtering both the rank-and-file and elite warriors of the Folk, you savagely push your way through to the final floor of the Sandy Barrens.
There, you are again stopped by the strange girl, who demands an answer to why Man has forsaken the pact between themselves and the Forest Folk. You are told that a long time ago, Man was forsaken and cast out of the Sacred Tree, cursed to live in the Outer Lands, while the Forest Folk lived in harmony within Yggdrasil. Growing more hostile, the girl flees into the forest. The discussions over, you are ambushed by the strongest warriors of the Forest Folk as well as their Guardian, the flying beast Iwaopeln. Defeating all of the warriors first, you proceed to confront the creature itself, eventually tearing it from the sky. After defeating the Guardian, the girl then appears to you one last time, lamenting the loss of her people. She tells you of the location of the next stratum, then curses you a final time before forever disappearing into the forest...
With that, you proceed back to Radha Hall to report your success in exterminating the Forest Folk. You are met by Subaltern Quinn, who notifies you that the Chiefain is currently somewhere in the Labyrinth itself, and asks you to keep an eye out for him as you explore. You then head down to the Sandy Barrens, where you find a hole leading to the next stratum. You go inside and see the decayed remains of what appear to be buildings: Lost Shinjuku.
You begin your exploration inside the ruined building, noting strange metallic doors, some of which open on their own and others which appear stuck. Exploring further, you find a piece of decayed paper with ancient writing on it. It speaks of something called the Yggdrasil Project and is written in a tense tone.
Crossing a broken tree connecting one building to another, you are surprised to find Ren and Tlatchga waiting for you in the center. You greet them, but both appear tense. They tell you that they have been given orders by the Chieftain himself to dispose of you to save Etria. It appeared that your guild was advancing far too quickly for the Chieftain's tastes, leading to the fear that if your guild continued to explore, the Labyrinth's mysteries would finally be solved... and Etria's one main draw and source of income extinguished. Not willing to back down, you draw your weapons for a fight. You combat the two women, who are more than able to hold their own against your team's combined might. After an intense battle, they eventually accept defeat. Handing you a Card Key, the exhausted warriors proceed to leave the area, promising to leave you to your own devices.
After healing up, you continue your exploration of the buildings, finding more aged, yellowed notes. As you continue to read them, you discover that it seems a scientist was working on an "Yggdrasil Project" to save humanity as a major environmental collapse drew near. However, as time wore short, both the man's family and friends perished, and he resolved to finish his project to save those who remained. The scientist's name is then revealed to be Visil...
You eventually reach the final floor of the Labyrinth, after repairing a contraption that allows you to quickly move between floors by turning on a 'generator.' Immediately after entering the area, a man's voice beings to taunt you, booming throughout the entire building. The voice challenges you to find him and discover the Labyrinth's true secrets. Fighting your way through hordes of monsters, you eventually reach a large set of locked doors. Swiping your hard earned Card Key and opening the door, you walk to the center of the large room where Visil, the Chieftain, is waiting for you.
He beings his story of how the world was in global peril back when he was still a scientist. After losing what was dear to him, he resolved to finish his project to save humanity by creating large trees that would eventually heal the world. However, knowing the incredibly long time it would take for his trees to do their work, he was not content in dying and letting the future care of itself. As such, he devised a way of 'connecting' himself with one of the trees, which granted him immortality but forever bound him to it. He waited for over 1000 years for the floods to subside and the terraforming of Earth to finish, where he then established the town of Etria and used the Labyrinth as a draw to help start and sustain an economy.
Finishing his tale, he tells you that you have unfortunately learned far too much to be allowed to live. Attaching himself to what appeared to be a control center of the tree itself, you are then forced into battle against the combined form of the Etreant. After a grueling battle, the Chieftain is finally slain, falling dead from his perch on his beloved tree. With Visil laying dead at your feet, you and rest of your loyal guild members resolve to never forget what you have learned, deciding to spread the truth of the Labyrinth...
After reporting your actions to Subaltern Quinn, he decides to reward your service to the Radha with a Town Medal. However, he also institutes a policy of silence regarding what happened to the Chieftain, feeling that the townspeople cannot handle the truth of what transpired. His suspicions are later confirmed as you speak to Etria's townspeople and hear nothing but concern for the missing leader.
Feeling lost not having a quest for the first time in a long while, you eventually decide to return to the 25th floor of the Labyrinth. Finding yourself drifting back to the room you battled the Chieftain in, you investigate the room further. Upon examining the back of a structure in the middle of the room, you discover a hidden stairwell. Gathering your courage, you step into the foreboding darkness below. As you head down, a blood-red atmosphere permeates your senses... it's as if you're inside a living being's organs. You find yourself in the Claret Hollows.
You return to Radha Hall and report your discovery to Quinn. He allows you to explore the final stratum, reasoning that a new challenge for explorers could help save Etria.
You undertake your final descent into the Labyrinth, fighting off what appear to be human-sized cellular organisms and monsters that are beyond the scope of anything you've fought before. As you continue, you find yourself following up on rumors and tales the townspeople held close. First is a battle with a Golem, a living statue guarding a long missing treasure. Next you find the Alraune, desperately ignoring her siren's call long enough to deal a deadly blow to the powerful member of the Forest Folk. You later find the bizarre, tortured form of the Manticor, a human chimera, and put the creature out of it's misery.
Pushing ever deeper, ever onward, you confront three extremely powerful dragons that have appeared within the Labyrinth. Utilizing your strongest skills and abilities, you challenge each of these mythical creatures: the fire-breathing Wyrm, the frost-blasting Drake, and the Volt-charged Dragon. After a long fight, you prevail against the destructive trio. Exhausted, you continue on, reaching the final floor of the Labyrinth.
Excited to be reaching the end of your long quest, you race through the dark, crimsoned halls of the Hollows, eventually reaching a door. You enter an empty room and head towards the back. There, you feel a way to push through the wall, but sense that doing so could mean certain death. Pausing for but a moment, you take the plunge into the wall. You find yourself in a wide room with a large beast standing guard at the only door. You challenge the beast, and quickly learn that it is an younger, adolescent version of the large Drake you fought. Defeating the Drakoid, you go into the next rooms and find a similar sight: the Wyrmoid and Dragoid. You dispatch them easily.
Finally, you enter what you sense is the final room in the entire Labyrinth. There, you are assailed by overwhelming terror as you behold a beast that only exists in nightmares, the core of the Labyrinth itself... Primevil. You fight an apocalyptic final battle, avoiding certain death only by utilizing every last trick and tactic learned from your many adventures. Pushed to the edge of your limits, your team barely manages to strike a killing blow to the Core. It falls, taking what feels like an eternity to drop to the ground.
You sense that you have truly conquered the Labyrinth... and as such, return to the surface, tired, scarred, but ultimately triumphant. You tell Quinn your incredible tale, showing him your progress in the Monstrous Codex and the Item Compendium. Truly impressed, Quinn informs you that you have completely filled out both records and hands you a Town Crown... and, with a hint of forlornness in his voice, congratulates you on conquering the Yggdrasil Labyrinth.
He wishes you luck on your next adventure.