One of Kelly's marines is about compete in a boxing competition. And he appears to be distracted by the girl he's seeing--Kelly's daughter. And Spoon's car is stolen and they find the thief and decide what to do with him.
Burner, Hammer and Kelly are on a carrier. Burner's plane loses radio reception and navigation after possibly being struck by lightning during a storm. Because of heavy rain he cannot see the carrier and he may run out of fuel and crash. Back on shore Spoon and Ice nearly become romantic before Capone alerts them about the danger Burner is in, whereupon they rush to base.
A Captain gives the team survival training. And some of the guys like Spoon is impressed with the guy. But the man asks Kate out and assaults her. She tells Ice who tells her to report him but she doesn't want to. So when they train Ice takes out her frustrations on the man. She then tells Spoon whose opinion of the man changes. Eventually Kelly learns about it and tries to help Kate.
Missiles are stolen from the base. Schaeffer, a Marine, saves Ice from a fire but when his burning shirt is torn off, a tattoo of a swastika is revealed and he is suspected of the theft. Meanwhile, Teri returns and guilt seems to keep her and Spoon apart. While Teri and Capone are present, Spoon uses a toast that Ice taught him on the night they almost became romantic.
The unit will be learning Burke's Breach, a combined attack strategem or set of tactics. General Burke, a former mentor of Kelly's, visits the unit, but his strange behavior endangers men during an exercise and Capone's career is threatened. Kelly discovers Burke's behavior may be caused by exposure to chemicals during the Gulf War.
Spoon and Ice go into a convenience store that's when a couple enter and try to rob the place. Spoon manages to get out but Ice is one of the hostages. The police arrive and there's a standoff. Kelly arrives but because of posse comitatus he can't do anything so he can only watch. At the same time Kate is having trouble with the guy who gives her her jukeboxes so Capone tries to help.
Capone's brother comes for a visit and Capone thinks there's more to his visit. Later the FBI shows up looking for him. They tell Capone that his brother went into business with a Russian mobster and his brother crossed him and now he's running from them.
Spoon gets a visit from an old friend whose lies put him in an uncomfortable position. The worthless son of a famed pilot causes problems on a mission led by Spoon and Ice. Capone arranges a photo shoot at the beach house with a bevy of scantily-clad women.
Spoon, Capone and Mad Dog decide to play golf. But it's while they're playing that Mad Dog is recalled to do some work. The guys offer to go back with her to give her a hand. Now a young marine found some unexploded ammo and decide to hold on to them and brings them to the base. When one of them goes off, Spoon and Mad Dog are trapped. When the Fire Chief arrives, he decides to take things slowly. Kelly is worried.
Kelly, Ice and Hammer go to an aircraft carrier for a mission. Kelly and ice go out on patrol while Hammer works with someone from the CIA. Kate learns that her husband was keeping a secret from her. She sets out to find out what he was keeping from her. But it turns out to be not what she thought it was.
When Kelly learns that one of his men is struggling to get by that his wife is shoplifting. He decides to go to Washington and to try and get Congress to increase his men's wages. He meets an old friend who works for the Senator who is in charge of that. But he has to contend with a defense contractor who wants them to buy his new device. Problem is they do, there won't be enough left for the wage increase. At the same time, the man whom Kelly is doing this for, gets in trouble when Doc Brandon thinks he is abusing his wife. And his wife turns to Ice for help.
When Spoon's mother is in trouble, financially, so Teri offers to help. And she thinks that an old associate of his father can help. He offers Teri and Spoon a job with him. While Teri wants to accept, Spoon doesn't want to give up being a Marine pilot. When a circuit board on a Hornet is defective, suspicion falls on maintenance Sergeant who installed it. And when other defective circuit boards are discovered and the Sergeant was the one who installed them, Kelly reluctantly relieves the Sergeant of his duties till the matter can be settled. His sister, a lawyer ...
After his daughter is injured in a car accident, Kelly takes her out on an plane trip to a remote cabin but the small plane starts having mechanical problems. They land, but have no way of calling for help and she starts having complications from the first accident and may die. Hammer, Capone and Ice try to find them.
There's an aerial combat competition going on and Kelly wants to win this one. And Ice finds herself face to face with the defending champion from the Air Force who's coming on to Spoon. Also former pilot and friend of Kelly's who now works for NASA has arrived. Everyone is assuming she's there to recruit someone for the next shuttle mission. Spoon is hoping he could be considered. But the woman is looking only at the female pilots including Ice. When word gets out Ice and the Air Force pilot are going at it.
Megan as part of her probation has to do community service and works at Make a wish foundation. And the boy whose wish she's trying to grant only wants to fly in a fighter plane. So she asks Kelly and he tries his best to grant the boy's wish. And Maddog meets a guy and hooks up with him but she later learns that he's married to one of the marines under her.
Kelly is informed that the unit has a mission and their liaison officer is Burner. Burner hooks up with Megan. And when a friend of Capone's dies in an accident, he behaves erratically. Kelly tells him he has to put himself together for the mission and gives him a day to do it.
Kelly's unit is on a mission which they execute perfectly. But Burner gets left behind. Kelly is ready to do what he has to to find him. But the man in charge, tells him, they have to pull out. And Spoon is feeling as if it's his fault that Burner got left behind.
When fears of a terrorist attack cause a special exercise to be delayed, the assassin sneaks away and becomes a threat to Kelly and Hammer. Kate returns, considering another's marriage proposal when she gets no encouraging signs from Kelly. Spoon and Ice's relationship heats up to the point that Kelly says one of them will have to be reassigned elsewhere.