As the Highlander arrives at the town of Etria, greeted by other adventurers entering the town, it is revealed that a group of Highlanders had been requested/invited to help investigate the mystery of the Yggdrasil Labyrinth. The leader of the tribe has decided to give the player the mission of solving Etria's mysteries. The flashback ends as he show a Radha Soldier a letter explaining the invitation from Radha. He is then allowed to go through, being welcomed into the town.
His first mission is to master cartography- apparently, all new explorers in Etria has to begin by taking on this mission. Ren and Tlachtga, a duo of Ronin and Hexer, are sent to help him on his first mission. After finishing, the three encounters a small short 'earthquake' before it goes away. They head back to report the results- the duo then leaves the Highlander, since he has now been allowed to explore the Labyrinth, having finished the beginner's mission.
The player is then sent to Gladsheim Area 1 to investigate, seeing as the Radha Hall thinks that the 'minor earthquakes' may be related to it. At some point, the Highlander finds a capsule containing a mysterious girl, and when he touches it, she was released from it. Right then, the player encounter a group of three explorers and the five are attacked by an Errant Cammel. The mysterious girl from the capsule decides to fight it, making the player engage in his first battle with a 'boss' (if considered one).
After defeating it, the girl states that her name is Frederica Irving, although she can't seem to remember anything. The group of three explorers reveal that they were researchers sent here by Midgard Library to investigate something; Simon (the Medic), Raquna (the Protector) and Arthur (the Alchemist). The five decides to team up and investigate Gladsheim Area 1 further, until they head back to Etria.
Later on, exploring the first Stratum , the group are tasked with the mission of slaying Fenrir, the leader of a dangerous wolf pack roaming in the Emerald Grove. By slaying it and its pack, the player and the others discover the path to a new Stratum. They also find a Geomagnetic Field there, to which they use to head to another area of Gladsheim Area 1. While exploring the ruins, they run into the beast Coeurl, who has the ability to turn invisible in darkness.
Defeating it leads to more questions, like why the 'terminals' or 'machines' reminds Frederica of the name 'Mike'. Deciding to dig up the mysteries, they learn that their questions may be solved by heading to Gladsheim Area 2- but a Geomagnetic Field can only connect to one area, thus the group decides to continue exploring the Primitive Jungles (second Stratum).
At some point, the Highlander and his companions are stopped from going through a specific door. Seeking permission, they take on the mission of retrieving the Wyvern's egg, which soon catches the interest of the Chieftain. By succeeding that, they are then tasked personally by Visil (the Chieftain) the task of slaying Cernunnos, a dangerous beast that they named with a God's name.
The player and his companions then manages to eventually defeat Cernunnos and uncover the path to the third Stratum, where they also find another Geomagnetic Field. Simon links it to Gladsheim Area 2 and the group explores it. However, although the answer to their questions lies right in front of the entrance, the power source seems to be damaged. By exploring the area, the five discovers that a bee hive was being built at the entire area- lead by the bees' queen, the Queen Bee.
As they defeat the Queen Bee, Frederica controls a terminal which finally lets power come back. The group of five returns to the entrance, where the answer awaits them. By activating it, the machine begins talking them, introducing itself as the Memetic Installation Keeper Engine , or for short, M.I.K.E.
As M.I.K.E. is activated, it easily recognized the voice of Fredrica, and guides her inside of his operating system in order to retrieve her memories. Once this process is completed, Fredrica, or as she would like to be known as "Ricky", states that she finally remembers her role for the Yggdrasil Project, and the dangers it currently posesses. The danger the Yggdrasil Project holds is that it would easily level Etria, and all of its citizens with it. Shocked, the group hurries back to town in order to tell Quinn and Visil about their new findings.
However, the Chieftan has ordered the genocide of the Forest Folk that reside in the Labyrinth. Once he leaves, Quinn notes that he had been acting strangely as of late, and encourages the guild to not do the mission dispite the Chieftan. Agreed, they set out to first find the Geomagnetic Field in the Sandy Barrens, the fourth Stratum of the labyrinth.
They find the Field easily, and is teleported to Area III of Gladshiem. Upon arriving, M.I.K.E. tells the group that since his activation, he has been able to erradicate most of the threats on the ruins in order to make exploring easier from this point forward, although he did admit that he could not destroy all of the foes. They take note of this and continue on their way to find his terminal.
Once it is found, Fredrica tells the group about the Yggdrasil Project, and the measures her generation took to prevent such an overgrowth of power from the Yggdrasil Core. This measure was called Gungnir, which while being the 'safer' of the two options, it would still destroy Etria. As she wishes to save both Etria and destroy the Core without sacrificing anyone, she tells M.I.K.E. that they would not be activating Gungnir. M.I.K.E., not understanding, promptly "shuts down", and Fredrica states that he just needs time to "think about it".
They return back to the fourth Stratum in order to continue on their 'mission', though they have reservations about it. They run into Kupala, who is both angered and confused about the party's position: They don't wish to harm the Forest Folk, though they will if need be. Kupala's statements that her fellow forest folk had been 'infected' did not seem to help in the matters. As the group explores the fourth stratum, they are sad to find that fighting with the Forest Folk would be inevitable.
They reach the last floor of the Sandy Barrens, where Kupala had been waiting for them. Again, the party tries to reason with her but their pleas fall on deaf ears as she calls her final Guardian, Iwaoropenelep. After defeating the Guardian bird, Kupala falls to the ground, defeated as she used the last of her power to summon the god, and simply asks that the party leave her to die. Regardless, they take Kupala to their guild house in order to get her strength back.
While they were back in town they report their mission back to Radha, and it is then that Visil forbids further exploration of the Labyrinth, though he does not give an explanation. Despite this, Quinn encourages that the party continues forth anyway, and to report anything directly to him and not to Visil.
Walking down the stairs to the fifth stratum, most of the party is shocked at what is before them. Large buildings made of stone and concrete which were now being overrun with plants and crumbling around them. The only one not surprised is Fredrica, who states with sadness that the area known as Lost Shinjuku was a town from her time called Tokyo.
Once again the party finds the Geomagnetic Field easily, and is transported to the fourth area of Gladsheim. Almost immediately upon entering the large, open room, a machine can be spotted in the upper area. Fredrica states that the machine is called Gimle, and it is Gladsheim's defense unit. Arthur gives the possibility that M.I.K.E. had used it to kill the enemies on the previous floor and in Gladsheim. They move around the room towards Gimle, in order to get to the panel it stood before to open a Moon door on the other side of the room where M.I.K.E.'s terminal resided.
As they approach the terminal, Fredrica once again tries to reason with him that Gungnir cannot be activated. Thinking that Fredrica was now going against their mission to destroy the Core at any costs, first offers that she once again goes inside the terminal in order to get her memories of the mission at priority. Failing that, he then activates Gimle in order to destroy them as they were now in his way of his mission.
While the battle is long an difficult, especially with the risks of getting close enough to Gimle to attack in the first place, the machine is defeated and Fredrica, for the last time, states that she is going to save both Etria and carry out her mission without Gungnir. This causes M.I.K.E. to temporarily shut down once again, only responding with one sentence to anything that was said to him. The group once again leaves Gladsheim in order to give M.I.K.E. space.
Once again back in the labyrinth, they run into Ren and Tlachtga, who are there to carry out Visil's wishes that no one were to go any further in the Labyrinth. While both sides are hesitant to do so, they engage in battle. Once the duo is defeated, they give the Highlander a key card which would be useful further inside. Exploring Lost Shinjuku gives the party a lot to take in, and after repairing a set of elevators, they reach a large door on floor 25. Using the keycard that was given, they enter and are immediately confronted by Visil.
Visil had expected them, and goes into a monolgue how he is Yggdrasil, that he was the founder of the Project, and that he would not let them escape with their lives for going to far to destroy him. He then morphs into a form known as Entreant, and they engage in battle. Visil, defeated and dying, gives Fredrica a vial of potion that would be the only thing that could weaken the Yggdrasil Core enough in order to defeat it. As he passes, the party give their condolences, and return to Etria in order to tell Radha Hall that their Chieftan was dead.
Everyone is understandibly upset by this news, and the party decides to end this once and for all. While they could not find the stairs into the next Stratum, they did find the Geomagnetic Field in the same room Visil had passed in, and are taken to the last area of Gladsheim in order to shut down M.I.K.E. at its core. However, when Fredrica tries to do so at the first terminal, she is denied, and M.I.K.E. is ready to activate Gungnir within 50 ticks. Alarmed, the party gets to the core terminal as fast as they possibly can and fights M.I.K.E. himself.
Succeeding defeating M.I.K.E. within their timelimit, Fredrica shuts him down completely. However she is heartbroken, as she essentially killed her friend. They return to town in silence and rest up at the Rooster Inn. In the middle of the night Fredrica leaves, but unknown to her was that the Highlander had followed her all the way to the final area of Gladsheim. She states, sadly, that she just wishes she could talk to M.I.K.E. again, because he was her friend. At that moment, the room lights up momentarily with the panel, but then fades again. The Highlander cheers her up, and that M.I.K.E. was saying goodbye to her. Now encouraged to continue on, they return to the Inn in order to sleep.
The party returns back to the second Geomagnetic Field in Lost Shinjuku, which Simon then changes its destination from Area V of Gladsheim to where he believed was where the Yggdrasil Core was residing. Teleporting to the 30th and final floor of the last Stratum, they find their way to the Core. The Highlander uses the vial that was given to them in order to significantly weaken the Core. After defeating it, the party congratulates themselves on saving Etria.
As they did so, however, the Yggdrasil Core had not been defeated for good, and had become more powerful than before--stated that the vial did not completely work. It is then that Kupala appears, her powers retored enough to help, saying that it was her duty to destroy the Core with her own power when the time came. She imbues the Highlander's spear with her power, and the battle against the Core begins again.
Now defeated--and defeated for good--on their way back to Etria they go their separate paths. Simon, Arthur and Raquna return to the Midgard Library in order to document their findings and adventures. Fredrica, deciding to stay alongside the Highlander, returns with him back to town to continue their adventures.