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After Col. Ballinger is injured during a traing exercise, Lt. Colonel Bill Kelly, a pilot, asked to take command of the Sea Dragons by Col. Rebecca Hodges. It is a four person team including First Lt. Robert/Bobby Griffin, a jet pilot; First Lt. Annalisa/ Analise Linstrom, a helicopter Huey pilot, First Lt. Wendell McCrae/McCray, a computer and electronics specialist and First Lt. A.J. Conoway/ Conaway an explosives expert.''''Their first mission is to save a DEA plane whose pilot has been injured in Central/South America. Meanwhile Bobby has started romancing Jeanine/Janine who is Kelly's daughter.
The druglord, Ramon Toledo, captured in the previous episode has a deal. He will receive an operation and a kidney from his brother, Miguel in return for information. This upsets Kelly, whose complaints, in turn, upset Dr. Valerie West. But the druglord has a hidden agenda. He has his brother's wife and children kidnapped so he can force his brother to help him escape. Bobby, who is in the hospital, from a minor volleyball injury, suspects something but has nothing concrete. Kelly goes with the team to a bar, the Tailwind, and discovers Janine is working there and sees that she is dating Bobby who is brawling with a guy who harassed Janine. Bobby learns who Janine's father is. The druglord sends Kelly and his team on a one way mission to rescue two DEA agents while he escapes with his brother and Valerie as hostages. It is up to Kelly and the Sea Dragons to survive and set things right.
When a pilot and his plane disappear with an experimental stealth device, he is suspected of being involved with a militia group.
A redhead, who made a pass at Bobby, drugs and murders a Strike Team Cobra for his security pass. She is part of a group of robbers impersonating Cobras who are stealing guidance plans. The Sea Dragons, who are unarmed, discover that their exercise has turned real when the robbers murder a guard. Also Linstrom has a date, Craig, and Janine goes out with Randy after seeing the redhead kiss Bobby.
The Sea Dragons are called upon when an African ambassador is suspected of stealing plutonium.
Conaway, Lindstrom and a third marine are hijacked by two men who have gambling debts. Conaway is shot and falls out of the helicopter and the others land on a small island. The third Marine is badly wounded but Conaway's wound is minor and he swims to the island and gets one of the hijacker's guns. However the criminal whom the hijackers owe arrives. Meanwhile Kelly, Griffin and McCrae are evaluating equipment from a sales representative whom Griffin romances. Griffin turns down her pass, however. The equipment may prove useful when they discover the others are missing and try to go on rescue mission.
The Sea Dragons try to protect two foreign dignitaries from assassination on their way to peace talks.
The Sea Dragons try to stop a biological weapon, a virus called the Grey Ghost, from being sold by arms dealers. Janine starts seeing an old boyfriend, Zach, because Bobby keeps breaking their dates for work reasons.
A man in Kelly's Vietnam unit is burned. It seems to have something to do with the accidental bombing of a village in which 30 or 40 civilians were killed. Kelly was in the hospital during the day of the raid. The operations officer, Joe Damian, got the coordinates wrong, and was tried, but considers himself a scapegoat. Kelly talks to another man from the unit, ""Jer"" Jeremy Britt who winds up dead from a car bomb. Kelly gets a photo of the bombing which is a threat that he is next. Janine's romance with Zach is interupted when Bobby happily horns in using the excuse that he is her bodyguard.
The Sea Dragons are sent to Korea to try and help get a defector across the border. Kelly's budding romance with Dr. West is interupted by the reassignment. Kelly decides to help Tomlin, a former navy man whose daughter is missing (she is being held prisoner by a nightclub.) McCray tries to romance a translator teaching him Korean. Robert finds out the woman running the nightclub is being tipped off by a pilot, Fingers, whom they thought was helping them. After they finish their mission the Sea Dragons rescue the girl too.
When a sheriff comes by investigating a former member of the Sea Dragons who washed out and his possible link to attempted shootings, the team takes leave to investigate. And Kelly seeks more parenting help from Dr. West.
The SeaDragons are sent in civilian clothing to investigate who hacked into a military computer. The ""company town"" they are sent to employs computer programmers and is developing software for the government. A.J. and AnnaLise kiss, albeit undercover. (As part of a cover story when they are discovered where they shouldn't be.)
During a rescue mission one of the pow's is killed and with his dying words he accuses Linstrom. She is placed on trial. Bobby dates a woman he met on the beach and spends the night with her. By the end of the episode AJ and Annalisa are necking.
The Sea Dragons are sent to rescue hostages in a Carribean nation but their efforts are endangered when a billionaire, whose daughter is one of the hostages, sends in a team of mercenaries to launch a frontal assault.
A test pilot, Peter Allenson, has problems during the testing of a new missle firing system. When the problems go unreported he warns Bobby who is about to test the system and he dies in a hit and run accident. Is there a problem with the system? Was Allenson murdered? The team investigates. Meanwhile Janine finds herself upset that her father is dating Valerie.
A.J. helps a pretty woman, Rita Garcia, by preventing her purse from being snatched. Then he finds the Naval Criminal Investigation Service suspects him of espionage. Meanwhile Bobby is competing against other pilots, including ""Hammer,"" for an instructor position.
Agent Catarez asks for the Sea Dragons' help in dealing with an arms dealer, Javier Nuñez (Nunez) entering the U.S. illegally. The arms dealer escapes but Bobby's father, Robert Griffin, is captured and was assisting him. Bobby tries to convince his father to help them.
A top secret experimental weapon that is missing from a USAF plane is found by a boy, Casey. The Sea Dragons are sent to recover the weapon but someone else is also looking for it. In their personal lives Janine goes apartment hunting and A.J. interferes when Annalisa flirts with a guy.
After a bird shatters the canopy of his jet, Griffin is injured both physically and emotionally, and may be permanently grounded.
In San Diego for a convention, the Sea Dragons must prevent the deranged Maj. Egan from stealing a laser weapon and taking vengeance against those he believes responsible for the deaths of his men.
While patrolling the no fly zone in Iraq, Kelly is shot down with Griffin in the back seat. While they try to avoid capture, the other Sea Dragons are frustrated in their attempts to help join the search and rescue. Back home Dr. Valerie West tries to reassure Janine.
After Seaton Palmer, an Irish terrorist with the R.F.I. is captured with nerve gas, Kelly and the Sea Dragons investigate. Annalisa Lindstrom and A.J. Conaway try going on a date. At the end of the episode Kelly is trying to decide which member of the team to let go due to budget cutbacks.
