After successfully arriving in the Spirit World, Korra and Jinora get separated. Jinora ends up at Wan Shi Tong's Library, where she is captured by Unalaq. Korra finds herself in a dark forest as a four-year-old, where she encounters Iroh's spirit. With the help of the former Fire Nation general, she helps a lost dragon bird spirit, who in turn helps her find the spirit portals. There, she is forced by her uncle to open the northern portal, lest he destroy Jinora's soul.
While on watch at the ancient meditation circle, Tenzin expresses his concern over allowing Jinora to guide Korra into the Spirit World, stating that he would never forgive himself if anything happened to her. Kya and Bumi reassure Tenzin of Jinora's capabilities, before taking a rest and allowing Tenzin to take first watch.
In the Spirit World, Korra reminds Jinora to be wary of dark spirits, before touching a flower which turns into a butterfly spirit. Intrigued, Jinora chases after it, prompting Korra to run after the young airbender. She inadvertently steps on a meerkat spirit, to whom she apologizes, before inquiring about the location of the Southern spirit portal. In the ensuing conversation, Korra reveals that she is the Avatar and is on a mission to close the portal which she had previously opened. While doing so, a multitude of meerkat spirits appear from the ground, telling Korra that they are not impressed and do not believe her claims. Frustrated, Korra attempts to use bending to fend off the spirits, but finds herself unable to do so. Angered, the spirits begin to attack Korra, who is slowly covered by a thick, purple goo upon impact. Alarmed, Korra calls for Jinora, who advises her to remain calm, as her energy is upsetting the spirits. Jinora attempts to save Korra to no avail, and the two are eventually swallowed by a sinkhole conjured by the meerkat spirits. The two find themselves underwater, and are promptly swallowed by a sea monster spirit. They eventually find themselves back on land, albeit being separated in the process.
Korra finds herself alone in a dark forest, where her emotions cause her to assume the form of her four-year-old self. Out of fear, she accidentally swats a young dragon bird spirit. Realizing this, Korra apologizes to the harmless spirit, and attempts to lead it out of the forest. Before she can find her way, she is startled by the voice of an old man, whom she recognizes as Iroh. The latter recalls his close relationship with Aang, before escorting Korra and the spirit out of the forest toward his teashop, to witness the marriage of May-Jim.
Meanwhile, Jinora ends up just outside of the forest, where she reunites with a much larger dragonfly bunny spirit, whom she recognizes as Furry Foot. Asking the spirit if it knew the location of the spirit portals, the dragonfly bunny prompts Jinora to mount it, before leading the airbender to Wan Shi Tong's Library. Amazed at all the knowledge stored in the building, Jinora claims that she could spend the rest of her life there. At that moment, Wan Shi Tong appears, remarking that the last person who made a similar comment was still in the premises, before motioning toward Professor Zei's skeletal remains. Despite Wan Shi Tong's orders for her to leave, Jinora pleads to be allowed to browse the library, offering wisdom in exchange for some time. The owl spirit refuses, doubtful of the fact that a young girl could offer him any new knowledge. Jinora is able to convince him upon explaining the true mechanics behind the radio, which Wan Shi Tong previously believed to have been operated by a small man inside the box due to some misinformation gathered by one of his Knowledge Seekers. He begrudgingly allows Jinora to stay, but warns her not to break anything, as he will know if she does so.
Unable to find a book detailing the location of the spirit portals, Jinora requests the help of one of the Knowledge Seekers, who provides her with an ancient tome that recalls the legend regarding Vaatu's imprisonment in the Tree of Time. Upon discovering that Vaatu will be able to break free of his bonds if the portals were opened during Harmonic Convergence, Jinora realizes that she must warn Korra, but is stopped by Unalaq before she could leave. Unalaq remarks how misguided Tenzin was for allowing his daughter to guide the Avatar into the Spirit World instead of himself. Jinora is surprised that Wan Shi Tong would help Unalaq free Vaatu, and the owl spirit reveals that Unalaq has shown himself to be a true friend to the spirits unlike the Avatar. In the heat of the conflict, Furry Foot becomes dark and restrains Jinora.
Back at his teashop, Iroh recalls how he decided to leave his mortal body following his death in order to live among the spirits in the Spirit World. He offers Korra some tea from a teapot that Korra immediately recognizes as hers, prompting Iroh to affirm her statement by recalling Avatar Wan's story, particularly about how he carried Raava in the teapot prior to the two's permanent fusion during Harmonic Convergence. In the middle of the conversation, Korra has an outburst, demanding to find Jinora, which causes the sky to darken as the dark clouds swirling above Hai-Riyo Peak to expand and the spirits nearby to turn dark. Iroh urges Korra to calm down and see how her energy is affecting the spirits, and she soon realizes that as the bridge between the two realms, her emotions have the capacity to alter reality and channel darkness. Inquiring as to how she would find her friend, Korra resolves to help return the injured dragon bird spirit to its nest atop Hai-Riyo Peak, after Iroh tells her that the best way to solve her problems is to help another.
After being led to the foot of the mountain, Iroh wishes the Avatar well, and urges her to visit him again, even in any following lifetimes. Korra begins to climb up the mountain, reminding herself to remain calm and unfazed, but is alarmed upon encountering a trio of dark lion dog spirits. Initially scared, Korra realizes that she must find the light within herself, in the process allowing the spirits to retain their pacified forms while also dissipating the storm clouds gathered around the mountain. The lion dog spirits help her scale the mountain, where she finally returns the dragon bird spirit back to its nest, where there are three others. The four dragon bird spirits merge to become an adult dragon bird spirit upon being reunited, and the spirit offers to serve as Korra's mount in gratitude. Her actions also allow her to return to her normal form. After climbing aboard, Korra tells the dragon bird spirit to fly toward the spirit portals.
After arriving, Korra approaches the Southern spirit portal in order to close it, but is stopped by Vaatu, who tells Raava of her impending defeat upon the arrival of Harmonic Convergence. Korra dismisses Vaatu's threats and continues toward the portal, but is surprised to see Jinora subdued by Unalaq. The chief threatens to corrupt Jinora's soul unless Korra agrees to open the Northern portal, and so she concedes, causing Vaatu's restrictive barrier to weaken in the resulting energy release. It's not until Unalaq nearly corrupts Jinora when Korra finally agrees.
After opening the Northern portal, Korra is attacked by her uncle, who taunts her about her inability to bend due to the nature of her entrance into the Spirit World before attempting his technique. Powerless to defend herself, Korra is unable to do anything as Jinora is carried away. However, before she is completely consumed by the purple light, Korra is saved by the dragon bird spirit, who attacks Unalaq and carries her away to safety.
Returning to her body, Korra is drained by the encounter and is horrified about what occurred. Tenzin rushes over and asks if she succeeded in closing the Southern portal and if his daughter was able to be of assistance. Korra, visibly shocked and distressed, apologizes to her mentor and looks to Jinora, enticing Tenzin to do the same. He is shocked to notice that Jinora had not returned and is still in the Spirit World, leaving her body to be in a comatose state without her soul. Tenzin, panicking and unsure what to do, turns to a tearful Avatar and asks what happened to his daughter.
The original Iroh appears in the Spirit World, and reveals that he decided to leave his body at the time of his death in order to live among the spirits. He owns a tea shop similar to the Jasmine Dragon, where he spends time with numerous spirits.
Unalaq uses a spiritual variation of waterbending to convert light energy into dark energy, turning spirits dark in the process.
The whale spirit seen flying when Korra and Jinora enter in the Spirit World was among the spirits fleeing from Raava and Vaatu's fight in "Beginnings, Part 1", and was later among the spirits led by the aye-aye spirit against Jaya and other humans in "Beginnings, Part 2".
Iroh uses a teapot that once belonged to Avatar Wan, which the latter used to carry Raava's weakened form prior to the second Harmonic Convergence in "Beginnings, Part 2".
Professor Zei's skeletal remains are seen in Wan Shi Tong's Library, where he decided to stay despite the structure's submergence in "The Library".
Wan Shi Tong declares that the Avatar is not a friend to the spirits, due to Aang's betrayal of his trust during their previous encounter.
When Iroh sips from his cup of tea after stating he made many friends in the Spirit World, the rim of the cup turned the same color as the swirl, whereas it has not every other time it is shown.
Iroh's advice to Korra about finding the light within herself parallels a similar piece of advice he gave Aang in "The Crossroads of Destiny", about finding the light at the end of a dark tunnel.
The circular design in the book Jinora looks through before asking a Knowledge Seeker for help is the same one used in the Book Two: Spirits trailer from the 2013 San Diego Comic Con.
This episode bears many similarities to "The Library", which was also the tenth episode of the second season of the first series. Both feature Wan Shi Tong and his library, as well as the abduction of a close companion of the Avatar that leaves them in tears.