This post contains lots of spoilers!!
Cassie (short for Cassiopeia because of course) is trying to survive an alien apocalypse. The book begins in the 4th wave, but there are flashback to the previous waves. The 1st wave was a huge EMP that turned off all electronics. The 2nd was massive flooding that destroyed most coastal cities. The 3rd was a plague that killed millions (including Cassie's mom). The 4th wave are Silencers - alien assassins that look like humans, which makes us unable to trust anyone else. Silencers killed her dad and took away her little brother, Sammy. She gets shot by a Silencer, but eventually is saved by a cute teenage boy named Evan. She stays with Evan until she recovers. He falls for her. She likes him, but still feels like something is a little off about him. She's determined to rescue Sammy, who she believes was taken to Wright-Patterson army base. Evan doesn't want her to go by herself and she agrees to let him join her.
Meanwhile, at Wright-Patterson, Ben Parrish (who, btw, Cassie had a huge crush on in high school) is sick with the plague and staying in the camps outside the base. The camps are attacked, but he's brought inside where he recovers from the plague. They convince him that some humans are actually aliens and that they can train him to fight them. He goes through training with other kids - some as young as 7! He's now known as Zombie. Eventually Sammy (aka Nugget) joins the squad too, but of course Ben doesn't know him. But they quickly become close. Their squad finishes first out of all the other squads and they go on a mission (except Nugget, he's deemed too young and has to stay behind to train more). On the mission, they figure out that they're not shooting at aliens - they're shooting at other humans! They have an eyepiece that helps them tell who's who but they realize it just shows them who has the tracker they were given or not. Ringer (the girl that Ben likes) convinces everyone to take out their trackers. Ben decides that he needs to go back for Sammy.
Cassie finally figures out what's weird about Evan - he's an alien! Apparently, some humans were implanted with alien consciousnesses when they were younger and they awoke a few years ago. Evan's job is to "cleanse" the earth of humans. But he fell in love with Cassie instead. She's freaked, but quickly becomes okay with it. She still decides to try to save Sammy, while he stays behind, just outside of Wright-Patterson. Action ensues, and Cassie and Ben basically get to Sammy at the same time. Evan finds them and saves them after they're captured by the aliens. Cassie and Ben escape with Sammy, but Evan stays behind to destroy the base. Just in time, Ringer comes back and saves Ben, Cassie, and Sammy.