This post contains lots of spoilers!!
Allie is looking for her sire Kanin because she can sense that he is in danger. He has been captured by an insane vampire named Sarren. Instead she finds Jackal, the raider king of Chicago who she tangled with in the first book. He is her blood brother, which is why she thought she was tracking Kanin when she was tracking him instead. Even though she hates him, she agrees to team up with him. He's looking for a secret lab that is supposed to be in somewhere in DC. If she helps him find it, he'll help her find Kanin. She's hopeful that Sarren brought Kanin to the lab and that they will find him there.
They find the abandoned lab. Sarren has been there and he has stolen samples of the Red Lung virus. Allie figures out that he is probably headed to the other lab that she knows is in New Covington, where she's from and swore she would never return. Jackal accompanies her back to New Covington. They sneak into the city and find that the human population has been infected with a virus that basically turns them partially into Rabids. They fight off a few and find an uninfected human. They force him to take them to the other human survivors who are holed up in the underground tunnels.
There Allie finds out that the leader of the refugees is Zeke, the human boy that she fell in love with but left in the safety of Eden. He has come to New Covington to find her. He is angry that she has apparently teamed up with Jackal, since he killed his adoptive father. After Allie explains why she's with Jackal, he understands. Zeke is determined that a relationship between the two of them can work, but Kanin always warned Allie away from that sort of thing.
Zeke decides to help Allie and Jackal get into the inner city, where they believe Kanin is. The plan is to pretend to be random vampires passing through and then sneak around and find and rescue Kanin. However, when they demand to see the Prince of the city, they are taken to his human assistant, who turns out to be Stick, Allie's friend from back when she was human. Stick believes that Allie turned on all their friends, causing their death. So much for anonymity. They are taken before the Prince of the city, who doesn't believe their story about Sarren being evil. But then Sarren attacks everyone, nearly killing the Prince in the process, and then escapes.
The Prince still refuses to release Kanin, because of his old hatred for him. But in the end, he agrees to release Kanin, but only if they promise to find Sarren. They still believe that Sarren has the cure for the new virus that has infected the city. But before they leave, the Prince gives Kanin tainted blood to drink from. They have discovered that if a vampire drinks from an infected human, they will get sick themselves. So now they have deadline.
Jackal appears to betray them and leaves. Zeke gets attacked by an infected human and becomes to sick to continue on with them. Allie reluctantly leaves him behind, hoping they can find the cure from Sarren. They are finally able to find Sarren, but he overwhelms them. Jackal is with Sarren, apparently siding with him. Sarren reveals that he has no cure - he simply wants everyone, humans and vampires to die so the world can start over again. Jackal ends up trying to help them and claims that he never actually betrayed them, he just wanted it to seem that way to trick Sarren. Zeke shows up to save the day and Sarren flees.
Zeke has apparently survived the illness. While he was in Eden, he received lots of vaccines and one of those must have protected him. Allie realizes that his blood is the cure and injects Kanin with it. Kanin recovers. They return to the Prince with vials of Zeke's blood and tell him they've found the cure. The Prince agrees to let them go as long as it works.
However, during the day, Zeke is captured. Stick admits that he sold him out to Sarren, who in turn critically injured him. They head back to the lab, hoping to find him. Instead they find an old laptop with an audio recording of Sarren killing Zeke. Allie is devastated and vows to never care for a human again. They believe that Sarren is heading to Eden. Allie, Jackal, and Kanin head there to try to stop him. The end scene shows Sarren heading off with Zeke, who is apparently still alive.