After a hurricane devestates a small Florida community, the sheriff calls for a quarantine. Meanwhile, a park ranger and his conspiracy obsessed brother-in-law make a strange find in the Everglades, leading them to begin an investigation. Also, the sheriff's wife and a priest spend the night of the hurricane outdoors and return safely, but changed.
Russell meets an Air Force officer with wounds like Dave's, and is drawn in to Dave's mystery. Mariel finds something odd protruding from those wounds.
A mysterious force leaves Jesse injured and unconscious, and when Mariel tries to help he only gets worse, leaving it up to Russell to save his son. Meanwhile, Dave investigates a mysterious piece of jewelry and Larkin begins looking into the strange events surrounding the hurricane.
A deadly variation of the flu is going around, and escaped lab animlas may be the culprits.
Russell looks into the strange circumstances relating to the shooting of a coworker.
After meeting a Cuban refugee whose family was lost to the "lights," Russell makes the decision to attempt to capture one.
Larkin has a near-fatal car wreck which could jeopardize her pregnancy, but a stranger's arrival in the midst of the accident produces some suspicions. Meanwhile, Mariel looks for a way to once again become a part of her son's life.
A woman denies that a baby abandoned at the ranger station is hers even though her mother-in-law says differently and Mariel makes a jarring discovery in the water.
After Russell becomes a prime suspect in a double murder, Larkin learns that her husband has a past criminal record - which leads her to question his integrity and investigate the circumstances surrounding it. Meanwhile, Dave contacts Mariel in an attempt to find out what happened to her the night of the hurricane, and Mariel pleads with Tom to dredge the bay to discover the true identity of the body she claims to have seen.
After reading his blog about the strange happenings in Homestead, Dave is abducted by a couple who have a vested interest in learning what he knows about the circumstances surrounding the hurricane’s aftermath. Meanwhile, Underlay and Sirk learn the identity of the dead woman found in the bay, and Sirk gets his first look at one of the orange, luminescent beings.
Mariel gets questions from Russell when she begins exhibiting strange new personality traits. Meanwhile, Jesse takes a trip with Rose and Larkin and finds himself mesmerized by a woman, and Sirk gets some assistance with the transition into his new life from Tom.
Russell discovers that Tom has taken the children on a vacation without bothering to get any kind of permission.
After being shot, Underlay looks back on the events of his rebirth. Meanwhile, Russell works against Larkin to try and stop word leaking about the hybrids.
A mysterious creature is discovered in the Varon home. Underlay is tracking down his shooter. Kira wonders what her father and Mariel encountered in the water.
Kira endangers herself trying to find out about her father.
Derek and pregnant Christina are armed, dangerous and on the run with Russel and Underlay on their tail.
Christina insists on Mariel having an ultrasound because of how fast her womb is growing.
Dave and Russell head to the island to do some digging for information. In the aftermath of the hurricane, the school students who were left affected and those left unaffected begin to clash, while Mariel attempts to unlock the military's secret doings with regards to the hurricane recovery.
Because of his investigation of the hybrids, Russell may lose his job. The hybrids sense a storm coming and prepare to take action. Jesse and a friend decide to try to get even with the hybrids.
The storm is rapidly approaching, so Russell and Underlay try to figure out where Szura has hidden the hybrids. They realize they will have to get their families out of Homestead.
The hurricane begins to hit Homestead. Russell and Underlay try to stop Szura. The National Guard rounds up Larkin, Mariel, and the kids for their protection, but Larkin and Mariel are suspicious of their rescuers. Dave is questioned as to the whereabouts of Underlay.
In the middle of the hurricane, Underlay and Russell attempt to rescue the humans who are being rounded up by the hybrids. However, two humans suspect that Underlay is the cause of the chaos, and they take Larkin, Dave, Jesse, and Rose as hostages. Larkin is accidentally shot, and Underlay takes her to the water.