In the balmy marsh of the Florida mangroves, Jim Longworth and Callie's son Jeff traipse through the swamp on a bug collecting excursion for Jeff's science class when they happen upon an abandoned private aircraft and a dead man nearby.
Later, as Jeff helps the crime techs secure the scene (which Longworth postulates is the result of a drug or arms smuggling operation gone wrong) Callie arrives, furious at him for exposing her son to a murder investigation.
As Jeff and Callie leave, Regional Director Colleen Manus shows up to rebuke Jim for trespassing on protected swampland. She tells Longworth he may be able to close cases, but she is aware he's damaged goods and will be watching him closely.
Assessing the body, medical examiner Carlos Sanchez puts the time of death at 72 hours from a single bullet at close range. Longworth adds that the plane they've found is probably stolen, registered to a couple of snowbirds from Seattle who have an alibi up north. Looking through the plane, Daniel Green (who is now interning for Sanchez thanks to his success with the last case) finds a bag of pig's feet marked with the name "Landing Strip Lounge." Longworth leaves to scope the place out.
Longworth describes the deceased to individuals at the lounge and learns the victim's name was Oliver "Ollie" Hendricks. Curt Powell, a patron at the bar and friend of Hendricks' from the Air Force, explains that Hendricks worked for Special Ops, but left the service a few years before and has been drinking and doing a little flight instructing ever since. Longworth questions Powell about his friend's Colombian connections and asks him about his own flying skills. Powell tells him he still flies, but only for fun these days.
At the squad room, Longworth finds Manus scouting out an office space right next to his own, presumably to keep an eye on him. Sanchez arrives with news that the Air Force is denying Ollie Hendricks ever existed, leading Longworth to believe he may be a secret agent.
The men use the cable company to track down Ollie Hendricks. As they search his apartment, Longworth finds a hidden gun of the variety that spies often carry. They discuss Manus as they work and Sanchez says he hopes their new boss will whip them all into shape. He also scolds Longworth for carrying on with Callie, who is married to a man in prison.
Suddenly, Longworth spots something in the corner of the room. It's a trip wire - one that's clearly been tripped. Moving through the apartment, the men determine someone has definitely been there before them. Hearing a noise, Longworth draws his gun and encounters a very frightened mailman. The mailman hands Longworth Ollie Hendricks' cell phone bill, which reveals a number of calls to one number. Longworth says he will ask Manus to extradite a warrant on the number's owner.
Longworth stops by Callie's house for a visit and meets Callie's gorgeous mother-in-law, Jody Cargill, who shuts him down when he asks to see Jeff and refuses to tell him where Callie is. As Longworth walks to his car, Manus calls to let him know the number they found on Hendricks' phone bill belongs to David Coulter, a man with no record or history who is likely another black-ops official.
Longworth and Sanchez storm Coulter's house with a team of Florida Department of Law Enforcement tactical agents in tow. The team enters the house to find David Coulter playing video games, not a black-ops official at all, just a 15 year-old boy.
David and his older brother Kyle are questioned about their relationship with Ollie Hendricks. David tells Longworth he met Hendricks while visiting the flight school to watch the planes fly, but Longworth can tell there is more to the story. He prods David until the boy confesses that he actually met Hendricks when the man caught him stealing a plane, though Hendricks never turned him in. David makes it clear that Hendricks only called him so many times in the past few days to check on him since he'd been having trouble with a boy at school and the two are simply friends.
Callie returns from a visit with her jailed ex-husband to relieve her mother-in-law, who's home with Jeff. Jody asks about her incarcerated son and also mentions that a Jim Longworth has stopped by to see Callie while she was out, off-handedly remarking that he should not be visiting a married woman. When Callie suggests it really none of her business, Jody takes it as her cue to leave.
Combing the swamp for more clues, Longworth circles back to the abandoned plane and discovers a live baby bird hidden in the instrument panel. Sanchez and Green take blood samples from the bird and learn it's a hyacinth macaw, an endangered parrot native to Costa Rica and the Amazon with a steep black market bounty. Longworth hypothesizes that Hendricks might have been using his special ops connection to deal in black market birds.
Longworth visits Bailey Saunders, a surfer and ornithologist friend of Green's, who confirms the bird is likely smuggled. When questioned about her own ties with black market bird smuggling, Bailey gives up the name of a former coke dealer, Eduardo Garcia, who used information she gave him to access both exotic pets and high-end collectors to turn a profit.
That night, Longworth chats up Garcia at a cafe. Garcia remains calm and cool until Longworth produces a photo of the baby bird. Reacting immediately, he tells Longworth to call his attorney, but the detective has the last laugh as he leaves without offering his name to a clearly shaken up Garcia.
On moving day at the office, Manus talks of her longtime fight to pin one of many murder, extortion and drug trafficking raps on Garcia. She thinks Longworth's method of arresting him on expired pet permits might just work; if they can link Garcia to the bird they can link him to the murder.
Later, Longworth and Callie discuss Longworth's large settlement, the result of being shot by his last captain, and Callie opens up about the difficulties of deciding whether to leave her husband, especially when his mother is still so much a part of her son's life. The two discuss Longworth's latest case and Callie wonders whether the good looking ornithologist Bailey Saunders and wealthy Eduardo Garcia who run in similar circles might've dated.
Longworth serves the warrant for expired pet permits on Garcia, who is smug and hints that the raid is actually the result of Manus' longtime desire to see him arrested. He also remarks that Saunders must be the one who gave him up, retribution for what was surely a lover's dispute.
Garcia continues to play it cool as Longworth searches his mansion which is filled with exotic birds and plants, all which seem to be protected by permits. That is, until Longworth spots a small hidden Newt, a highly endangered and illegal bird - enough ammo to arrest Garcia and search his place.
Garcia and his lawyer Malcolm White, friend to drug dealers and other dangerous characters, argue that a slight offense like a permit violation will never land Garcia in jail, however Manus argues that abuse of the Endangered Species Act will get him audited for all his property, plus 5 years in the pen. His back against the wall, Garcia fingers Bailey Saunders, who, as it turns out, has a hundred acres of property in Costa Rica which Garcia claims she uses to capture illegal macaws. Still, Longworth suggests, the 125 pound Saunders never could've actually murdered someone. Garcia laughs, asking if they've ever seen her handle a machete.
Daniel interviews Bailey, a bit taken with her. Looking at Daniel's eye, Bailey realizes he's contracted pink eye from handling one of the wild parrots in evidence. She tells him she will get him eye drops and Daniel swoons. Watching from the interrogation room, Longworth sends the already love-struck Daniel home.
Going into the interrogation room himself, Longworth questions Bailey about her land in Costa Rica. She confesses that while she donated the land to the government as a natural reserve, she was using her dual citizenship to smuggle birds with Ollie and Garcia from Costa Rica to the US, but insinuates that it was only possible because she had someone else on the American side with special access.
Putting the pieces together, Longworth questions Ollie Hendrick's friend Curt Powell at the Landing Strip Bar about his part in the bird smuggling ring, but before he can get any details, Powell leaves the bar (presumably to take a phone call) and flees the scene in a small plane, just as Longworth suspected he might.
When Powell is captured, he confesses that he provided coordinates to Ollie to help him fly in undetected with the birds, but balks at the idea that he murdered anyone. Longworth presses him, explaining that he knows Powell has been taking calls from Garcia, prompting Powell to further give up that when he arrived as part of the plan, Ollie was already dead. Longworth asks Powell why he should believe him and Powell explains that neither he nor Ollie was certified to fly anything more than a twenty-five horsepower and that the Cessna (the plane found with Ollie's body) is rudder controlled, making it hard for someone like Ollie with a bad knee to pilot for that long. This new information gets Longworth thinking...
Examining the body, Carlos determines Ollie's knees were in fact too weak to fly the abandoned plane. He also tells Longworth he's determined the prints on the plane's steering column are from none other than David Coulter, Ollie's 15-year old friend. David explains that he did sit copilot for Ollie during a bird run but went right home on his bike once they got back to the reserve. Longworth isn't buying it and suggests that David's brother Kyle actually picked David up under the impression he could get some of the smuggled goods, but when he tried to steal from Ollie, the man fought back and got killed in the process. To confirm he's suspicions, Longworth removes Kyle's sunglasses to find that he has pink-eye, a sign he's been touching the illegal birds.
Kyle admits he killed Ollie and David flies into a fit of rage, though Kyle claims it was just an accident. He leads Fish and Game officials to the stolen birds, which were hidden inside a foreclosed home where Kyle was keeping the stolen birds, hoping to sell them.
The men run into Manus back at the office who is heading out to catch Eduardo Garcia's trial, knowing they finally have enough evidence to put him behind bars.
Later, Longworth plants a rare cicada (courtesy of Daniel) in his house to entice Callie to bring Jeff over to finish his bug-collecting project. Callie notices a new surfboard propped in the corner and quickly deduces it must be a gift from the swimsuit model-type bird expert Longworth spoke of earlier. The two share an awkward beat as Callie tells him that sometimes what seems like a beautiful new challenge can often end up more trouble than it's worth. They both question whether they are still talking about surfing as the sexual tension mounts between them, just in time for Jeff to say he's got his stuff and is ready to go home.