Team Avatar and Tenzin's family travel to the Southern Water Tribe to attend the Glacier Spirits Festival. While there, Korra's uncle, Unalaq, attempts to persuade Korra to let him advise her about the spirits, but both Korra's father and Tenzin assert that she needs to focus on her airbending. However, during the festival, Korra discovers that it was her father and Tenzin rather than Aang who kept her locked away, and after a Dark Spirit attacks, Korra breaks off her studies under Tenzin and takes up Unalaq as her instructor.

Korra begins her spiritual training under Unalaq. The first step of this training is to travel to the South Pole and open up the spirit portal residing deep within the area. Mako, Bolin, Tonraq, Desna, and Eska come along as well. Tensions between Korra and her father grow as she discovers the truth about his relocation to the Southern Water Tribe.

Korra tries to remain neutral as tensions flare between the Northern and Southern Water Tribes. However, things are complicated when the Southerners are talking about preparing for war and a group of rebels try to kidnap Unalaq. Meanwhile, at the Southern Air Temple, Tenzin, Bumi, and Kya all search for Ikki who has ran away after being teased by her siblings.

In an attempt to get Judge Hotah to release Tonraq, Korra discovers that Unalaq had set up the trial and his brother's banishment, causing her to break away from him and his teachings. Meanwhile at the Southern Air Temple, Tenzin finds Ikki and they reconcile with their respective siblings

Korra attempts to gain support for the Southern Water Tribe from the United Forces, but her request is denied by President Raiko. As a result, she, Bolin, Varrick, and Asami attempt to take matters into their own hands and devise a scheme to send military troops to the South Pole behind the President's back. However, brewing tensions between Korra and Mako complicate things.

When criminal activity threatens to put Future Industries out of business, Mako sets up a sting operation in an attempt to arrest the culprits. The plan backfires, however, as it drew them away from the company's warehouse when it was being robbed. Mako investigates further and discovers the true culprit.

In order to cleanse herself from a dark spirit's attack, Korra must reconnect with her Avatar Spirit by finding Raava. To do so, she needs to learn about the origins of the first Avatar, Wan. He tells her how he received the power of fire and learned the ways of the spirits, as well as how he was the one responsible for unleashing Vaatu, the spirit of darkness, into the world.

Wan's spirit shows Korra how he learned the other three elements and the reason why he eventually merged with Raava and became the first Avatar. His story makes Korra realize what she must do to restore balance to the physical and spirit worlds.

Korra seeks Tenzin's help to enter the Spirit World for the first time. However, their attempts prove to be futile until Jinora comes to Korra's aid. Meanwhile, Mako and Asami rekindle their relationship, though Mako's investigation into Varrick's affairs lead to the firebender's arrest.

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.

Bolin saves the day when President Raiko is mysteriously attacked in Republic City. With Mako arrested, Asami tries to free him and learn who is framing him.

With the help of her closest friends, Korra must close both spirit portals before Harmonic Convergence occurs.

Korra learns of a new twist in Unalaq’s evil plans to release the spirit of all darkness and evil, Vaatu, from his longtime imprisonment in the spirit world.

Unalaq has finally merged with Vaatu and is terrorizing Republic City in the form of a giant spiritual monster. Without Raava or any prior Avatar connections, Korra must meditate and find the cosmic energy of the universe within herself in order to defeat Vaatu.