Five years after the fall of Galbatorix, peace had seemingly fallen over the land of Alagaësia. Halen, a young woman living on the island of Illium, was in the midst of tracking lovuk — giant, wolf-like creatures native to the island — that had been behaving irrationally in recent months. However, her efforts were thwarted by the bewildering sight of a Nïdhwal, a fierce sea creature, battling with a crimson dragon. When she spotted the dragon's rider unconscious in the water, she reacted without hesitation to save his life, bringing him back to her remote village for healing.

The local medicine man recognized the dragon rider as Murtagh Morzansson, who went into self-exile after Galbatorix's reign came to an end. Although his reasons for turning up in the far southern isle were a mystery, Hal and her guardian, Denu, sought to save him, regardless of his past. When Murtagh finally awoke, his attitude and demeanor indicated that very little had changed for him since he's been isolated from society with only Thorn for company. Insisting that he has business elsewhere, Murtagh expedited his healing with magic until he was strong enough to take off on his own.

Expecting life to return to normal after meeting a dragon rider, Hal was instead thrust into personal turmoil when a group of her closest friends went missing during what had been a standard hunting trip. In tracking their whereabouts, she ran into Murtagh and Thorn once again, who revealed the real reason they're on the island: Murtagh's half-brother, Eragon Shadeslayer, had a series of dreams — much like when he once dreamt of Arya — where he sensed a little girl was in danger. Unable to leave his post in the far east, he reached out to Murtagh to aid in the search.

They decided that going after Hal's missing friends together would be advantageous for them both. It's then that they run right into two Ra'zac and two letherblaka. Murtagh and Hal are both rescued by Hal's friends and run for cover. But Hal was singled out by the Ra'zac because of her scent and was captured and tortured for information. By the time Murtagh arrived to save her — led by a mysterious spirit — she was revealed to be a powerful magic user. Murtagh succeeded in saving her life, and the events softened his demeanor towards her. Especially when he sees the scars on her back from a whipping she received as a child.

Pressured by Thorn to continue Eragon's investigation and to help Hal overcome this new hurdle of being a magic user, Murtagh agreed to stay in the village and even to teach Hal how to use magic. Months passed where the two became good friends. Realizing they have more in common than expected, their kinship grew into something precious, a source of happiness for them both. Murtagh and Thorn also found companionship in the other villagers as well. And when it comes time for him to leave, he chooses instead to stay, much to everyone's delight and relief.

However, after months of silence from the Ra'zac, Hal's mind is suddenly attacked by an unknown presence. She managed to protect her mind and her identity, but not without the help of the spirit from before, that fortified her mind even further. However, the spirit leaves Hal with a single warning: It is time. She is coming.

Meanwhile, with Murtagh having disregarded to check-in with Eragon, two elves, Blödhgarm and Invidia, arrive to assist. Thanks to Hal's defenses when her mind was attacked, everyone begins to realize they are likely dealing with a Shade. With this new information, the elves insisted on taking over Hal's training. When a neighboring village is attacked by Ra'zac, it is revealed that Hal can use magic without the ancient language, a feat believed impossible until now.

With the strain of the growing mystery surrounding them, Hal and Murtagh grow closer until they finally share a kiss. But Hal's happiness at this new development isn't enough to dissuade the guilt she feels, and she finally revealed the truth of her past: her village on Uden was occupied by Galbatorix's soldiers when she was 10-years-old. When she accidentally killed a soldier using magic, she was punished with a severe whipping. Her father, in defense of her, killed another soldier. They retaliated against the entire village who tried and failed to defend their homes. They were slaughtered in the night, Hal's parents and younger sister, Thea, among them.

Finally deciding that enough was enough, Hal, Murtagh, Blödhgarm, and Invidia descended into the tunnels — where Hal was first captured and tortured — after she realized that the Ra'zac had been using them to get around the island to avoid the sunlight they hate so much. However, the Shade had set a trap for them, and Hal is forced to separate from the group in the hopes of sparing their lives. But just before she runs off, she finally confesses to Murtagh her love for him, fearing she may not get the chance to do so again.

The tunnels take Hal all the way to Uden, where the Shade reveals herself to be the sister Hal believed perished twelve years ago. Neither had suspected that the other had been alive all this time. And the spirits that have been helping Hal weren't there by accident; they're actually the souls of the Sani who lost their lives all those years ago. Conjuring ancient and powerful magic, Thea uses the spirits against their will to force Hal into becoming a Shade. However, Hal's appearance doesn't change and she became the first ever Shade who could still pass for human.

In Thea's effort to turn Hal fully, she managed to locate the Tenari village, letting Ra'zac run loose amongst the people. Thea waited for Hal's frantic return only to kill Denu right in front of her. The casualties are a grim reality, and Hal and Murtagh make the painful decision to leave so that the village might be spared from further attacks. But Hal has promised the Sani that she would stop Thea by any means necessary. And the journey ends with Hal, Murtagh, and Thorn fleeing to the mainland in the hopes of finding Thea before she finds them.