A hurricane is quickly approaching a small town in Florida leaving the residents little time to prepare. When the hurricane finally hits, many of the residents' lives are in peril. Rose, one of the town's smallest residents notices some mysterious lights in the heart of the hurricane. Meanwhile, after the storm, Dave discovers some mysterious skeletal remains.

Russell and Mariel suffer a tragedy but it is made worse when Mariel tries to help. Kira feels guilty over an accident. During the hurricane and after there has been a mysterious military presence and Larkin tries to learn more about it. Meanwhile, Dave investigates a lost piece of jewelry.

The citizens start to question why the town is still under a quarantine that has cut off medical and building supplies. The citizens find themselves on the verge of a major medical pandemic. Russell and Sheriff Underlay must track down the source of this quickly spreading virus.

A family of Cuban refugees tries to make their way to Miami. After they notice the lights in the water, their escape from Cuba is cut short. The next morning Russell encounters one of the Cuban survivors. Meanwhile, Mariel attends a support group and Larkin realizes that someone is following her.

Larkin barely survives a car crash and the fate of her unborn baby is unknown. Larkin gets picked up by a stranger in a pick-up but she soon becomes suspicious of his motives. Meanwhile, Mariel tries to reconnect with Jesse.

Sheriff Underlay tracks down a mother who has abandoned a baby at Russell's ranger station. The mother denies that the child is hers. Her mother-in-law swears that the baby is her grandchild and that Christina has been acting strange ever since the hurricane hit. Meanwhile, Mariel who begins questioning why she has been losing touch with her kids makes a shocking discovery in the water.

Russell is suspected of committing a double murder. Larkin discovers Russell's criminal history and wonders about who he really is. Mariel insists that she saw a body in the water and demands that the bay be dredged.

Russell, Larkin and Dave find out the identity of one of the creatures. Meanwhile, Underlay tries to find out who shot him and Kira begins to wonder what really happened to her dad.

Russell and Tom team together to try to catch a pregnant Christina and Derek, who are armed, dangerous and on the run. While searching Russell and Tom find a group of migrant workers. Mariel confides in Jesse and Rose about what happened to her. An unconscious Kira is in the hospital after her encounter with the orange being. Larkin searches for more answers about Paxton and his real reason for being in the area during the hurricane.

After his investigation of the hybrids, Russell finds that he may be out of a job. Sensing another storm, the hybrids prepare. Rose's teacher is teaching a subject that has Russell bothered. Jesse and a school friend find a way to get even with the hybrids.

Russell and Underlay find that they have to work together as another storm is quickly approaching. They need to get their families out of Homestead and to try to find where Szura has stashed away the hybrids.