While Kenzi, Hale, and Dyson, are all living their lives, Bo is nowhere to be found. It's later realized that they simply forgot Bo, as someone was forcing them to. Massimo has been giving Kenzi temporary powers to appear Fae. Bo finally awakens to find herself on a train, and later jumps off. A group of Fae called the "Una Mens" are introduced. When she arrives home, it is discovered that while Bo herself did not consciously choose a side, her blood has chosen Dark. Tamsin is found reborn, as a little girl, and grows up with Kenzi as her pseudo-mom. Massimo steals from Bo and Kenzi in an attempt to convince Kenzi to pay him, and Bo figures out that he is not Fae, but human. He also kidnaps Tamsin to acquire her Valkyrie hair, and after being defeated by Bo, chases after the hair into a pit of lava, where at that point he is assumed to be dead. Many of Trick's secrets and past actions are revealed, including a tie to a past life of Tamsin's, and the fact that he used his blood to "erase" someone from existence. Tamsin discovers that by not taking the soul of a man named Rainer to Valhalla, she is part of the reason "The Wanderer" was created. Bo is able to get back on the train, where she finally meets Rainer, and brings him back to the Dal. Hale and Kenzi admit their feelings for each other. Lauren, who has been working with the Dark, somehow turns the Morrigan human. Kenzi's mother is introduced, and Hale attempts to propose. Massimo returns, and protecting Kenzi, Hale is killed. Kenzi tries to get revenge, but is stopped by Vex, who mentions that he is Massimo's guardian. Evony is revealed to be Massimo's mother, and gave him to Vex years ago when he was a boy. Bo learns that not only is her father coming, but that to close the portal, she will need to give her heart. That is revealed to be Kenzi, who sacrifices herself. It ends with Bo visiting Kenzi's grave.

With Fae society in upheaval, Bo finds herself facing further changes and challenges as former ally Hale becomes the acting Ash – trying to forge a new balance between Light and Dark by appointing a Valkyrie aligned with the Dark Fae, Tamsin, as Dyson's new detective partner. Meantime, Tamsin is a secret agent working for two separate clients: The Morrigan, who wants to build a case against Bo so that she can execute her; and as a mercenary for someone who wants to entrap Bo. Matters become complicated when Kenzi is kidnapped by a crazed Kitsune who assumes her identity and deliberately sows distrust in the relationships between Bo and those closest to her, just as Bo must prepare for and go through an evolutionary Fae rite of passage that forces her to explore her past and future. Danger escalates when a human scientist convinces a despondent Lauren to join him in conducting scientific research in his private laboratory – all the while deceptively concealing his intent to harness Fae genetics for himself with the use of her expertise. The third season culminates with Bo being engulfed by black smoke and disappearing into thin air, presumably whisked away by her mysterious and powerful biological father (who may be "The Wanderer" that recurred throughout the season's story arc).

Bo faces personal challenges with Dyson after she finds out The Norn took his ability to feel passion for her in exchange for giving her the strength to defeat Aife in the season one finale; and with Lauren when their relationship became complicated after The Morrigan informed Bo in "It's Better to Burn Out Than Fae Away" that Lauren had a girlfriend. At the same time that she is coping with these turmoils, a villainous and evil ancient enemy of the Fae, the Garuda, is awakened and reappears with the intent to destroy the truce between Light and Dark Fae, and reignite the Great War between them. The new Ash, Lachlan, recruits Bo to be his champion in the battle against the Garuda and she agrees on the condition that he regard her as a partner, not as his servant. During this hectic time, Bo develops a no-strings-attached lustful relationship with Ryan Lambert, a Dark Fae Loki playboy that in "Fae-nted Love" became unwittingly thralled by her when, during energy-drawing healing sex, her blood came into contact with deep scratches she made on his back. Bo learns in "Into the Dark" that she is not only Trick's maternal granddaughter, but deduces that she has inherited some of his Blood Sage powers: if her blood comes into contact with someone's open wound, it can enslave and bind the recipient to her will (the same power that her mother, Aife, used to create male slaves). She uses her blood power to unite her team of Light and Dark in the final battle against the Garuda.

Bo is a Succubus who grew up in an adopted human family, unaware of her non-human nature and of the Fae world she descended from. She began to feel "different" when she entered puberty and didn't know she was not normal until she accidentally killed her high school boyfriend by draining his life energy during her first sexual encounter. When she told her parents what had happened, they broke the news to Bo that she had been adopted (see "Raging Fae"). Not knowing what she was and what she had done, Bo hated herself and ran away from home, exchanging her previous life for one without family or friends, moving from place to place and assuming a false identity whenever she killed again.

In the first episode, Bo saves a young human woman, Kenzi, from a rapist who had surreptitiously drugged her with a "roofie" in her drink. The two quickly become friends and Kenzi decides they should team up to create a Fae/Human detective agency. Confronted by the Fae leaders of the local territory with a demand for her to choose a side – either "Light" or "Dark" – Bo declares herself neutral, deciding instead to side with humans after Kenzi risks her life to find out where Bo had been taken by force and what they were doing to her. Most of the Fae considered Bo an unknown entity that should either be eliminated as a risk to their secret existence or exploited for their benefit. Throughout the season, Bo learns more about the Fae world and herself while she searches for information about her origins. Along the way, Bo also develops romantic relationships with both Dyson, a Light Fae wolf shapeshifter and police detective; and Lauren, a human doctor and scientist in servitude to the Light Fae.