An undercover agent, Hays, assigned to gather evidence against Syndicate head John Lawton, is blinded in an explosion. Lawton's lieutenant Deetrich and his business advisor Matula are rivals - Matula is actually an IMF undercover plant - so the IMF must keep him from being exposed and make sure he takes Lawton's place. Lawton believes Hays is working with someone in his organization. Jim, surgically blinded, takes Hays' place. Lawton has his henchman Brown watch Jim and then offer him money to reveal the leak. Deetrich pays Jim to finger Matula but in the final showdown Matula plays Lawton an IMF-supplied tape of Deetrich and Jim planning to implicate him. Deetrich and Brown are killed in the subsequent shootout and Lawton and Matula leave, telling Barney (infiltrated in as a mobster) to take care of Jim.
Kroll and Stevens run the Northeast Syndicate and the IMF must bring them down. In '37 the two of them killed a rival mobster, hid the body, and killed the witnesses, so the IMF needs to get Kroll to lead them to the remains. They grab Kroll, drug him up, and cosmetically alter him to look like he was in '37. Then they dump him on a Hollywood set and convince him through incredibly elaborate means he is in 1937 on the day of the murder and the rest of his life is a dream. Overwhelmed by the sheer amount of detail, Kroll and ""Stevens"" reenact the murder at a cafe, which gives them the location so that Barney and Willy can find the real body in the real cafe's basement. The IMF fade away, leaving a reaging Kroll to confront his partner as he flees the 1937 New York set and wanders into an adjacent Old West street.
Alex Pierson, a rising Syndicate member, has recruited Dr. Burke, a psychopathic behavioral psychologist who has developed a way to program men into killers. Pierson lures in underworld criminals with an offer of plastic surgery and turns them over to Burke, who programs them to kill Pierson's targets three times then kill themselves. Barney infiltrates as a crook on the run but when he fails to dose himself with a counter-drug, he is converted into a psychotic killer as well. They lose contact with Barney - Jim plants evidence on Burke making him look like he's turning against Pierson and another IMF agent made up to look like Barney goes after but fails to kill Pierson before fake-killing himself. Pierson confronts Burke while Jim gets the info on Barney's location out of Burke's assistant, and Willy stops the tech expert from killing his target in the nick of time.
Syndicate boss Delaney controls the waterfront and eliminates any potential witnesses - the IMF have 72 hours to bring him to justice before the grand jury closes. Barney infiltrates Delaney's waterfront organization and sabotages it, while Jim is a captain of a Norse ship, The Orion, on which Delaney once killed a man. Casey poses as the dead man's daughter and tries to implicate Delaney. The team capture Saunders, Delaney's killer, and Barney then claims to be employed by Delaney's Syndicate liaison Morgan and forces Saunders to set up a meeting on-board the Orion. Saunders ""escapes"" and warns Delaney, and they kill Morgan. The Syndicate head Mr. C is also present, lured to the ship, and witnesses the killing. He leaves one of his men to kill Delaney but the police arrive and Delaney testifies in return for protection.
Only two Syndicate men know where $8 mil in heroin will be arriving - narcotics dealer Alvin Taylor an dhis executioner, Frank Kearney. When Jim approaches Kearney to make a deal and he refuses, Willie ""shoots"" Kearney - Barney as a surgeon then operates providing a heart transplant and covertly uses drugs and hypnotism to make Kearney mild-mannered. Kearney can't bring himself to shoot Jim and hears on the radio about people taking on the traits of persons they received organs from - with the aid of new girlfriend, the church-hating Kearney finds out the man who donated a heart was a priest! Realizing he can't do his job and the Syndicate will wipe him out, Kearney leads Casey and the rest of the team to the beach where the heroin drop occurs, and the police arrive just before Taynor can kill Kearney.
Berlinger, a millionaire manufacturer and stolen gem dealer, will be transferring diamond to a Syndicate boss for $75 million. Only one man knows where the diamonds are - Hoffman, Berlinger's former lieutenant, who stole them. Berlinger is torturing Hoffman for their location. The IMF must get the gems and the money. Barney springs Hoffman and they become partners so Hoffman dives for the gems (hidden on the body of a courier sunk at sea). Casey brings Berlinger to Jim, posing as a diver, who offers to get the diamonds. Willy follows Hoffman to the gems and the team knocks him out and takes him into custody - then Jim leads Berlinger to the same spot and offers to make a deal in return for his $5 million payment. Under pressure from the Syndicate, Berlinger agrees and in the subsequent meeting the police capture everyone.
An earthquake damages the U.S.'s Distant Early Warning (DEW) system and a Defense Department advisor, Whitmore Channing, steals plans from the Air Force identifying the weak spots. Channing has hid the information for pick-up by an enemy agent the next day, and the IMF must get the name and flight # of the agent from Channing. The IMF evacuate Channing's city block and drug him unconscious after a fake electrical shock, then wake him up after adjusting the clocks to a day later. He believes the information has already been picked up, an idea ""proven"" by a faked IMF invasion of the European People's Republic. But then the EPR invaders arrest Channing and put him on trial. Channing reveals the location of the drop to prove his ""innocence"", and then the IMF let him covertly know the whole thing is a fake. Channing calls his contact and mentions his name - the IMF get it via a tapped line and arrest the man before he can recover Channing's info.
Stu Gorman is a music-industry figurehead for the Syndicate. He and his financial expert, Belker, are taking control of the music industry and the IMF have to stop him. The IMF know that Gorman killed a witness, Judy, to keep her from testifying, so Barney auditions for Gorman using a song called ""Judy's Gone Now"" and claiming Judy had taped Gorman when he killed her, and he has the tape. Barney gets Gorman to pay blackmail while Willy fake-rigs Belker's car to explode and claims he's working for Gorman when caught. Belker gets lead to Jim as a corrupt policeman with the recording, and he and Jim agree to blackmail Gorman instead. The IMF gives Belker a fake tape of the murder scene and when Belker confronts Gorman, Gorman knows its a fake and admits he killed Judy, then tries to kill Belker. But the police show up - the IMF have Gorman's confession on tape.
Publisher Granger is controlled by the Syndicate, killing reporters and protecting Syndicate-owned politicians in his state. The IMF must make sure the voters know what Granger is up to before the next elections. Appealing to Granger's interest in UFOs and his obsession with immortality, chauffeur Barney hits him with a paralysis drug delivered by bee sting and Jim and Casey mysteriously appear in a light show, ""cure"" him with futuristic equipment, and appear. Thanks to IMF-rigged reports of UFOs, Granger believes they are aliens! After another rigged death of Casey that Jim ""cures,"" Granger begs for immortality. Jim agrees if he publicly renounces his way. Granger exposes the Syndicate candidates and then is shot by his former aide and Syndicate man.
Wendell Hayes, the brother of an imprisoned Syndicate enforcer, has stolen a canister of nerve gas and threatens to use it if his brother Cayman isn't freed - the IMF must stop him and recover the gas. Worse, the canister has a defective casing that Wendell is unaware of, and will release the gas in 43 hours anyway. And...Cayman dies of a heart attack in jail, forcing the IMF to have guest-agent Bill Williams take his place. The IMF has Hayes' imprisoned girlfriend Saretta ""escape"" with prisoner-Casey handcuffed to her. Saretta takes Casey to a winery in a IMF car with a bug on it that Barney traces. Jim delivers ""Cayman"" but Hayes doesn't turn over the gas. They track Hayes to an observatory but he gets word via his partner Tully that his brother tied and he unmasks Williams-as-Cayman. Hayes and Tully shoot it out over an argument and with his dying breath Hayes tries to shoot open the canister...hid in the observatory roof, revealing its location to the IMF.
Syndicate members Trask and Mason control the Syndicate's illegal racing operations, while Trask ruthlessly dispatches the competition - the IMF must take them out. Trask is jealous of thoroughbred owner Mason so Jim offers him a mysterious but promising racehorse - Trask finds out the horse is a kidnapped fast-racer. The IMF arrange for him to get the horse and then place a number of bets on the horse in Trask's name. After keeping Mason from having the horse killed, Trask's horse wins and the IMF get the $4 million from the Syndicate funds, leaving Trask to hold the bag.
Joe Corvin, a Syndicate money handler, ships millions through Swiss banks and the IMF must put him out of business. Corvin uses a courier that the IMF set up - Corvin has him killed and needs a new courier. Casey steps in as his mail-order bride addicted to drugs by airline employee-smuggler Jim. Corvin and Jim become partners but when the IMF fake-tightenes up security, they need a new way. Casey fakes her death and Corvin ships the cash in her coffin. Barney steals the money and the coffin is dropped on the runway, revealing a fake corpse. Corvin is confronted by the Syndicate, and an alive Casey shows up with two tickets to Miami. The Syndicate let Casey go and dispose of Corvin, permanently.
A private detective, Edison, has pictures incriminating Syndicate boss Vochek in a murder and is using them to blackmail the mobster. The IMF need to get the pictures to get Vochek convicted, but Edison has been convicted and is in prison for six months. Since Edison is unaware that his accomplice Leona is dead, Casey takes her role while Jim is Edison's cellmate and helps him to escape, then fake their deaths. Casey-as-Leona tells Edison she sent the evidence to the D.A. after she heard Edison was dead, and Jim convinces Edison she is keeping the pictures to pull off her own blackmail scheme. When Edison confronts her, Jim fake-shoots her but she calls a confederate to get the film - desperate, Edison reveals the location himself as he goes for it, and ends up arrested.
Syndicate boss Chandler's alibi is provided by Lt. Governor Harrison, who is in Chandler's pocket. Chandler has the husband of the only witness, Nora Dawson, get her committed and proceeds to have her driven insane at a mental hospital he controls. The IMF must get her out and have her testify in 24 hours. Jim gets Casey committed and she is put in a room near Nora, then he manages to get to Nora's cell and she and Casey switch - Jim then takes Nora-as-Casey out. The team get Nora off the island - when Casey-as-Nora is called to testify, she babbles insanely but then removes her mask while the team bring the real Nora in to testify.
The Syndicate is bribing a major politician, codenamed ""C6"", through their operatives Harry fife and his chief killer Jenkins. The IMF must find out who C6 is and get the evidence against him. Fearing a IMF man he had killed got too close, Jenkins recommends someone new, Jean Royce, to make deliveries. Barney takes Jenkins place while Casey becomes Royce. Fife gives Casey a bag of explosives to deliver to C6 to silence his payoff demands for good. Barney finds out but is exposed and wounded, but warns Jim and Willy...but an accident destroyed the tracer. Jim allows Jenkins to escape and return to his boss, then visits Fife himself as a Syndicate head and tells him that C6 must stay alive. Fife sends Jenkins to warn C6 and reveal Casey is a cop, and Jim traces the call and Willy saves Casey just in time.
Syndicate boss Orin Kerr runs the casinos and the IMF needs to get the evidence against him to put before the state legislature. Kerr's boss distrust him because of his extravagant lifestyle and Syndicate man Cameron plants a bug in Kerr's office, which the IMF taps into. The IMF then set Kerr up with fake conversations that make him look bad to his bosses - Cameron hears Casey and Kerr discussing a heist of the vault, and Jim shows up with a background indicating he pulled off a similar heist 12 years ago. Barney manages to steal the money out of the impregnable vault while Kerr thinks he can get the missing money from Jim's earlier bank heist by putting him into debt at the casino. Kerr follows Jim to the hidden money which is actually his own) and grabs it, and then Cameron shows up and demands to know why Kerr has carrying current currency. Dumbfounded, Barney intervenes and Kerr flees into the arms of the police, where he is forced to testify against the Syndicate in return for pr
An $8 million army payroll has been stolen from a base in SE Asia by the Stafford family, Syndicate drug smugglers. The IMF must recover the money. Jim and Barney steal a Stafford truck and then offer to sell it back to the family if they pay ""protection."" Jim meets with brother Doug to convince him brother Art has ordered a hit on Doug - however, Art has put a hit on Jim and he is ambushed and gets amnesia. Meanwhile, lounge-singer Casey meets with Doug and sets it up so he thinks Art is trying to kill him. Doug makes a deal with Barney for protection from his brother in return for $2 million and leads the IMF to the money - they arrest everyone and convince Art to tell them about his plan to kill Jim. Meanwhile Art's killers are on Jim's trail and when Barney gets hold of him, he manages to recover his memory just in time to thwart them.
