Eragon, Roran, and Saphira travel towards Helgrind, the shadowy mountain dwelling of the Ra'zac where Katrina is being held. They infiltrate the mountain, rescuing Katrina and killing one Ra'zac and both of their flying parents; but Eragon secretly finds Sloan, who was tortured and blinded for information, but finds that he cannot bring himself to kill him. Telling Roran and Katrina that Sloan is dead, he sends them back to the Varden on Saphira, and remains in Helgrind to kill the remaining Ra'zac and rescue Sloan. The last Ra'zac attempts to strike a deal with Eragon, informing him that Galbatorix has almost found "the name", in exchange for him keeping alive the memory of the Ra'zac as the monsters of humanity's nightmares. Eragon refuses the deal and kills it. Later, while deliberating his course of action regarding Sloan, he discovers Sloan's true name and, thus, gains great power over him. Instead of killing Sloan for his betrayal, Eragon, after consulting with the elvish Queen Islanzandi, decides to place enchantments on the butcher that will allow him to reach sanctuary with the elves, on the punishment that he never see Katrina again and attempts to rectify his ways. If he does, the elves agree to restore his sight.
Arya, who went searching for Eragon after he fails to return with the others, meets Eragon in the town of Eastcroft and return south, where Roran and the villagers of Carvahall who had not settled in Surda have joined the war.
Roran informs Eragon that he and Katrina wish to marry, and that Katrina is pregnant. The day of the wedding, a small unit of 300 soldiers from the Empire, including Murtagh and Thorn, attack the Varden. Again, Murtagh is difficult to beat with an apparent source of supernatural energy aiding him, but Eragon, Arya and twelve elven spellcasters are able to combine their powers and best him: he retreats, but vows to return stronger than ever. Orrin, King of Surda, and his cavalry, meanwhile manage to destroy the enemy army, but discover that its soldiers are immune to pain, and can suffer the most grievous wounds without dying: only decapitation or severe organ damage stops them. Roran and Katrina's marriage is then completed.
Nasuada orders Eragon to attend the election of the new dwarf king as a member of Durgrimst Ingeitum, Saphira remaining behind in case Murtagh attempts to attack. Eragon is reunited with Orik, the new clan-chief of Durgrimst Ingeitum. An attempt is made on Eragon's life by Dûrgrimst Az Sweldn rak Anhûin, a clan who declared hostility towards Eragon and Saphira. Orik has the clan's leader who orchestrated the attack banished, and thanks to the attempt on Eragon's life he is elected the new king. Saphira then comes to Tronjheim, where she and Eragon are reunited.
Meanwhile, Roran becomes involved in many Varden attacks on the Empire, all of which he acquits himself well in, showing distinct bravery and skill. However, in his second-last engagement, he is assigned to an incompetent general, Edric, who orders a full-scale charge into a force far bigger than the Varden and one that would have caused mass death and defeat. Roran refuses to let his regiment do this, tactically using archers and killing almost two hundred men himself, which saves most of his men and entirely destroys the opposing force, but to the disgust of the troops he saved, he is later punished for his insubordination with fifty lashes on the whipping post. Later, Nasuada comes to him, apologizing for the necessity of the punishment, informs him that Edric has been decommissioned, and requests that he now take command of an entire force. Urgals, a warlike but not evil race most of the races of Alagaseia despise, are amongst this group since Nasuada had earlier allowed their assistance before the Battle of the Burning Plains (Eldest), but the alliance is crumbling because of the mutual distrust of both races. Roran has to battle one of the Urgals to assert his authority during his first command, winning against a far stronger opponent; the Urgals under his command do not question his leadership again and, later, fight alongside him at the siege of Feinster.
Eragon and Saphira return to Ellesmera to see if Oromis knows how Galbatorix and Murtagh are so powerful. There, Eragon learns that Brom, his former mentor, was his mother's paramour and Eragon's true father, who fell in love and worked together to undermine and bring down Morzan, Galbatorix's right-hand man and his mother's former lover. The next day, Eragon is told the source of Galbatorix's power: many "heart of hearts", or Eldunari, a gemlike organ which can contain a dragon's consciousness indefinitely if separated from the body and gather energy from an unknown phenomenon. Glaedr explains that Galbatorix controls hundreds of these, taken from dragons he slew during the Fall, and these are the source of his power and presumably that of Murtagh. Eragon finds a deposit of rare celestial iron used to make Rider's swords, and makes himself a new sword, under psychic direction from the fabled elven smith Rhunön, who swore not to make weapons after the Fall. Eragon names the sword "Brisingr", with the unexpected result that it emanates fire, its namesake, every time Eragon says its name.
Glaedr gives his Eldunari to Eragon and Saphira, who leave to help the Varden's siege on the Empire city Feinster, while Oromis and Glaedr fly to aid the elves in Gil'ead.
Eragon and Saphira join the siege, where they are reunited with Arya. They find the leader of Feinster, Lady Lorana who is forced to follow Galbatorix but still requests assistance from Eragon and Arya to stop Feinster's magicians from creating a Shade to wreak havoc on the Varden. Arya kills the Shade with some assistance from Eragon, and with the surrender of Lorana, Feinster is taken. During the siege, Glaedr's heart of hearts sends his experiences to Eragon: During a battle against Thorn and Murtagh (who is later possessed by Galbatorix) Oromis and Glaedr are both killed, but Glaedr's grief ravaged consciousness endures within his Eldunari, which Eragon keeps. After the battle, Eragon reveals to Nasuada the existence of the Eldunari as well as the death of Oromis. Eragon's liegelord is heartened by the revelation of Galbatorix's dependence on the Eldunari and the weakness it presents, and announces that the Varden plan to march to Belatona, then to Dras-Leona, and finally to Uru'baen to dethrone Galbatorix. The story ends with Eragon relating how he feels lost in the absence of a mentor, but is comforted by the fact that Galbatorix has at least one weakness which they intend to exploit in the upcoming confrontation.