The story opens with Eragon, Roran, and Saphira travelling towards Helgrind, the dwelling place of the Ra'zac where Roran's betrothed, Katrina, is being held prisoner. They infiltrate the city, rescuing Katrina, but Eragon also finds Sloan, her father, who had betrayed Carvahall to the Ra'zac in a nearby cell, barely alive. He is faced with a moral dilemma: should he kill Sloan in cold blood or not? Eventually, needing time to plan, he tells Saphira to go back to the Varden with Roran and Katrina, who think Sloan is dead, while he further explores Helgrind and plans what to do with Sloan. He eventually decides that he will force Sloan to go to the elves with the permission of Islanzadi and will be banished from seeing Katrina ever again. He is very unhappy with this, urging Eragon to kill him instead , but with the revelation of Eragon discovering and speaking his true name, he goes.
Eragon then begins to journey back to the Varden, taking great care as he passes through the cities. Meanwhile, Saphira has arrived back at the Varden, and Arya, concerned for Eragon's safety and whereabouts, has set off in pursuit of Eragon. Arya and Eragon meet up again, and together they escape the city and return to the Varden, where Roran asks Eragon if he will marry him and Katrina in two days' time. Eragon is flattered, and agrees. He then mines three gold spheres with magic, and gives one to Carvahall's leather hide tanner whose hides he had stolen when leaving Carvahall, then one to Jeod's wife, Helen, in the hope she will start up a business and prosper in her accustomed wealth. He also allows Jeod to ride Saphira, and Jeod tells Eragon of his father, Morzan, and his mother, Selena. He also visits the Varden's weapons master. On the morning of the wedding, a small batallion of soldiers from The Empire march on the Varden, who are puzzled at the size until they see Murtagh and his dragon, Thorn, and conclude that the army is only a small distraction and their real intention is to capture Eragon. With the help of elf spellweavers that have been assigned to aid and protect him, Murtagh is driven away. The marriage takes place that evening, and Eragon gifts Brom's horse, Snowfire, to Katrina and Roran, as well as two magical rings that will help them when they need it, and allow them to always know where the other is.
No sooner are Eragon and Saphira reunited, however, when Nasuada orders Eragon to attend the election of the new dwarf king. She tells them that Saphira must remain behind, for if she didn't and Murtagh learned of it, he would crush the defenseless Varden. Eragon reluctantly leaves her behind, with the conditions that Saphira be permitted to come to the new king's coronation, and he be allowed afterwards to go and continue his training with the elves, and they mourn the severance of their connection. Once again among the dwarves, Eragon is reunited with Orik, the new clan-chief of Durgrimst Ingeitum ("Clan of Smiths"), and his new wife, Hvedra. When the counsel starts to vote on the next king or queen within the clans, the power struggle between the thirteen of them soon becomes evident. Debates on unrelated topics, such as farming land allocation, are debated over for far longer than Eragon is comfortable with, especially in Saphira's absence. We also see the story from Saphira's point of view during this time in which she seems very lonely. Soon after, an attempt is made on Eragon's life by unknown dwarves, which is investigated and found to be the work of
Az Sweldin rak Anhuin, ("The Tears Of Anhuin") who have shown open hostility and anger towards Eragon and Saphira. Orik presents this evidence to the clan-chiefs and a vote is taken in Orik's favour. Therefore, he becomes the new dwarf king. Eragon and Saphira are joyously reunited. Much to the dwarves' delight, she mends the Isidar Mithrim ("Star Rose") that she and Arya had shattered in rescuing Eragon from Durza in the first book.
Eragon and Saphira then return to the Varden, and then from there go to Ellesmera, the elves' capital. When they arrive at the hut of their masters, Oromis and Glaedr, Eragon becomes frustrated at the fact that neither of them divulged the knowledge they had that Morzan was his father. But then, Glaedr tells him that Morzan was never his father, but Brom. He is also told about the source of Galbatorix's power. A 'Heart Of Hearts' is a dragon's heart, which can contain their consciousness if separated from their body, and exist forever. Glaedr explains that Galbatorix has hoarded and controlled hundreds of these for many years, and these are the source of his power. They also discuss Eragon's need for a new sword- the weapon he had been fighting with was unsuitable for a Rider. He tries a dead Rider's sword now belonging to one of the noble elf families, but it does not suit him very well and he turns it down. He visits
Rhunon, a master craftswoman, who he asks to forge a new blade for him, but she refuses, saying that he would need a special material called brightsteel before she would consider forging one. Remembering how the werecat Solembum had told him 'When the time comes and you need a weapon, look under the roots of the Menoa tree', Eragon retrieves the brightsteel and, using his body, she forges him a new sword, which he names Brisingr. Unusually, anytime he speaks its name, the sword will burst into flames. He continues to be instructed by his tutors, and when the time comes to leave to help the Varden's siege on one of the Empire's cities, he is amazed to find that Oromis and Glaedr are leaving it too. Oromis explains that the time has come to oppose Galbatorix directly, joining Islanzadi in Gil'ead, which he can now do because he has finished his task of instructing Eragon. Glaedr gifts his Heart of Hearts to Eragon and Saphira, just in case he and Oromis are killed, before they go their separate ways.
Eragon and Saphira join the siege, where they are reunited with Arya and rescue her from attacking soldiers. Eragon and Arya race to find the leader of the city, who they hope to keep hostage. However, she informs them that magicians have decided that they know the city will fall to the Varden: they just want to create as much as possible - so they have set about trying to create a Shade. Horrified, Eragon and Arya race to the magicians, slowly bypassing their wards and killing each one in turn, but one transforms before they can reach him. Eragon and Arya fight him, with Arya eventually stabbing him in the heart. While fighting him, however, Glaedr's heart of hearts sends messages of Oromis and Glaedr fighting Murtagh and Thorn in Gil'ead, which has been attacked. Oromis dies in the fight, while Glaedr is driven to death with grief. The story concludes with Eragon telling Nasuada about all of his training, and the fact that he is not Morzan's son. Eragon feels hopeless, but is then comforted in the knowledge that he has hope, and many comrades in his fight against Galbatorix.
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