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 with Kya and Bumi, 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. His siblings reassure Tenzin of Jinora's abilities, 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 runs after it, and Korra, running after the airbender in turn, inadvertently steps on a meerkat spirit. After apologizing, she asks about the location of the Southernspirit portal. In the one-sided conversation that follows, Korra tries and fails to convince the spirit that she is the Avatar, on a mission to close the portal. As she talks, a multitude of meerkat spirits appear from the ground and bombard Korra with blunt skepticism and disbelief. Frustrated, Korra attempts to use bending to fend off the spirits but finds herself unable to do so, having meditated into the Spirit World. Outraged, the spirits attack Korra by throwing themselves at her and transforming into a thick, purple goo upon impact. Alarmed, Korra calls for Jinora, who advises her to remain calm, realizing her energy is upsetting the spirits. Korra fails to calm down, and the two fall through a sinkhole created by the meerkat spirits. Suddenly finding themselves underwater, they are swallowed by a sea monster spirit and fall into a spiraling river, where they are each pulled in different directions by the water. They eventually find themselves back on land, albeit at different locations.
Finding herself alone in a dark forest surrounded by dark spirits, Korra's emotions cause her physical form to revert to that of her four-year-old self. Out of fear, she accidentally swats a young dragon bird spirit and injures its wing. Realizing this, Korra apologizes to the harmless spirit and gently picks it up. An old man approaches carrying a lantern and, noting that they seemed lost, offers his help. When Korra realizes she recognizes him, the man tells her of his close friendship with Aang, prompting her to remember his name: Iroh. He leads her and the spirit from the forest to his teashop, where they attend a tea party in honor of the marriage of May-Jim. Iroh offers Korra tea from Wan's teapot, and Korra immediately recognizes it as hers, prompting Iroh to state that when she was Avatar Wan, the teapot had housed Raava before the spirit's permanent fusion with Wan during Harmonic Convergence.
Meanwhile, Jinora finds herself just outside the forest and reunites with a large dragonfly bunny spirit, whom she recognizes as Furry Foot. Asking the spirit if it knows the location of the spirit portals, the dragonfly bunny prompts Jinora to mount it and takes her to Wan Shi Tong's Library. Amazed by the amount of 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. Despite the fact that Jinora revealed the true working of the radio, as Wan Shi Tong had been under the impression they were operated by small men within the radio itself based on faulty information gathered by one of his Knowledge Seekers, he did not change his mind. However, upon discovering that she is a descendant of Aang, he relents and allows her to stay, warning her not to break anything.
Unable to find a book detailing the location of the spirit portals, Jinora asks one of the Knowledge Seekers for help, and it provides her with an ancient tome, which recalls Vaatu's imprisonment in the Tree of Time. Upon discovering that Vaatu will be able to break free of his bonds if both of the portals are open during Harmonic Convergence, Jinora realizes that she has to warn Korra but is stopped by Wan Shi Tong and Unalaq, who declares Tenzin to be a coward for allowing his daughter to guide the Avatar into the Spirit World. Jinora asks Wan Shi Tong his reasoning for allying with Unalaq, and he explains that Unalaq has shown himself to be on the side of the spirits, something Korra has failed to do. When Unalaq asks Jinora to come with him to see Vaatu, Furry Foot becomes dark and forcefully restrains her.
Back at his teashop, Iroh recalls how he decided to leave his mortal body following his death, so that he might live among the spirits in the Spirit World. In the middle of the conversation, Korra becomes upset over losing Jinora and throws a tantrum, which causes the world around her to change: the clouds above Hai-Riyo Peak darken and expand, and the spirits nearby become dark as well. Iroh urges Korra to calm down and to see how her energy is affecting the spirits. 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 can find her friend, Iroh tells her that the best way to solve her problems is to solve the problems of another, and Korra decides to help return the injured dragon bird spirit to its nest at the summit of Hai-Riyo Peak.
After being led to the foot of the mountain, Iroh wishes the Avatar well and urges her to visit him again, even if in a following lifetime. Korra begins to climb up the mountain, reminding herself to remain calm and unfazed, though is alarmed to find a trio of dark guardian spirits standing in her way partway up the mountain. Despite her initial fear, Korra realizes that she must find the light within herself; succeeding in doing so, she returns the spirits to their pacified forms while also dissipating the storm clouds gathered around the mountain. The guardian spirits help her scale the mountain, and reaching the top, she returns the dragon bird spirit to its nest, where there are three others. The four dragon bird spirits merge to become an adult dragon bird spirit, who offers to serve as Korra's mount in gratitude. Korra's actions also made her to return to her normal, adult form, and she climbs onto the spirit's back, telling it to fly to the spirit portals. The spirit immediately takes off, the three guardian spirits following in their wake.
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 initially dismisses Vaatu's threats and continues toward the portal, but when Vaatu threatens Jinora's safety, Korra turns to see Unalaq holding Jinora captive. The chief threatens to corrupt Jinora's soul unless Korra opens the northern portal. Korra advances on the duo though when she reaches the base of the Tree of Time, her progress is thwarted by a dark Furry-Foot. Looking around, Korra notices that the three guardian spirits have returned to their dark form as well. Korra blames Unalaq for deceiving her, making her believe he wanted to restore balance with the spirits. Pointing out that turning the spirits dark is not balance, she demands him to release Jinora. Dismissing Korra's demand, Unalaq makes it clear that Jinora will only leave the Spirit World alive if both portals are open. When Jinora begs Korra to refuse, Unalaq increases his hold on her, coming near to completely corrupting Jinora to emphasize that he is not bluffing. Unwilling to sacrifice her friend, Korra concedes and opens the portal, causing Vaatu's restrictive barrier to weaken.
Mere seconds after opening the portal, Unalaq assaults Korra with his waterbending, noting that she should have entered the Spirit World through the portal if she had wanted to retain her bending. Weaving through her uncle's waterbending attacks, Korra makes her way over to where Furry-Foot is holding Jinora though before she can truly reach them, the dark spirit takes off with the young airbender. Korra gives chase though is knocked over and captured herself by the dark guardian spirits. Seizing his chance, Unalaq raises his spiritbending water around an semi-unconscious Korra, attempting to destroy her spirit. Before he can do so, however, the dragon bird spirit whom Korra saved swoops down upon them, knocking Unalaq off his feet with its tail, sending him tumbling. The spirit takes Korra, almost unconscious and powerless, in its talons and flies away from the portals. As she is carried off to safety, Vaatu calls after Raava, announcing that he will be free from his prison once Harmonic Converge arrives to have his revenge.
Returning to her body, Korra pants in exhausting as Tenzin rushes over to her. As she is being asked what the Spirit World was like, whether Jinora was able to help her, and if she managed to close the portal, a distressed Korra merely manages to utter a weak apology, averting her eyes to Jinora. Tenzin follows her gaze, seeing Jinora's motionless body. Desperately clutching his daughter, a mortified Tenzin turns to Korra and asks for an explanation.
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 book 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.