At a gathering of high-ranking Soviet Union officials in Moscow, General Marenkov (Robert Shaw), the head of the government security agency K.G.B, reveals that there has been a breach of Project Winter Harvest, a plan to establish a Soviet network of biological warfare devices throughout Europe. After the meeting, Marenkov requests that the Project's Director, Colonel Nikolai Bunin, travel to Zurich, Switzerland, to assist in trapping the suspected culprit, a spy known by the code name Angelo.At a train station in Switzerland, a team of American intelligence agents, led by Colonel Harry Wargrave (Lee Marvin) and his associates, Elsa Lang (Linda Evans), Leroy (Joe Nameth) and Neckerman (Arthur Brauss), retrieves the latest cassette tape sent by their Soviet informant Angelo. The tape is discreetly transferred among Wargrave's team until it reaches the hands of Haller, the superior officer, who is waiting on a private jet. After decoding the recording, Haller, Harry and Elsa listen as Angelo announces that this tape will be his final one and requests that the Americans meet him next Friday in Milan, Italy, during the noon tour at the La Scala opera house. Angelo explains that the position of the militarist hardliners is becoming more powerful in the Soviet Union, and subsequently Project Winter Harvest has been reactivated under the leadership of Bunin. With his cover threatened, he plans to defect immediately.Three days later during the opera house tour, Harry and Leroy wait for the rendezvous with Angelo whom they have never met. Suddenly, from behind the curtain of a private box, Marenkov reveals himself to be the informer, Angelo. While escorting Marenkov to a safe house in Milan, the Americans subdue and foil enemy agents who try and stop them. Because Marenkov is the third most powerful official in the Soviet Union, Haller suggests they need to bury him in a missile site to protect him. On the contrary, Marenkov wants to give the Soviets and Bunin a chance to come after him, which will expose the Soviet network of elite undercover agents and provide the Americans with a chance to defeat Bunin and Winter Harvest.Meanwhile at a covert location in Zurich, Bunin receives a telegram from Moscow reporting that the attempt to trap Angelo in Milan failed; therefore, Bunin must assume control of the European clandestine network consisting of Soviet agents planted under the deepest cover. Bunin updates Rudi Muehler, who has nurtured this network for years and is reluctant to hand it over, that Marenkov is the spy Angelo. Since Marenkov possesses the most classified information, his defection is not a routine intelligence operation but a political crisis. In order to kill Marenkov, Bunin must have access to Muehler's elite agents and issues orders for them to be war-ready.Back at the Milan safe house, Harry proposes that they accompany Marenkov on the Atlantic Express train from Italy to Holland. Despite the risks, Harry persuades Haller that the scheme could flush out Soviet agents who have been in reserve for over twenty years, as long as they can keep Marenkov safe as bait. Through a series of decoys, the American agents sneak Marenkov on the train at the Milan station and keep him under close guard; however, Soviet agent Olga (Sylvia Langova) soon delivers intelligence to Bunin about the plan. Bunin orders Muehler to organize an attack, and confidently tells Olga that he already has two undercover agents positioned in separate cars of the Express.After crossing the Swiss border, Harry and his team encounter a unit of Soviet agents who have seized a signal tower along the route, but they defeat the Soviets in an exchange of gunfire that knocks out most of the compartment windows. As the train nears a Swiss mountain pass, an area helicopter communicates with the Express about possible inclement weather.On the Wasserhorn summit, the pilots notice skiers, but they are actually Soviet agents who set off explosive charges, creating an avalanche. The pilots warn Harry that the only option is to take shelter in the upcoming tunnel, but the train operator cannot increase speed and make the tunnel in time unless three wagons are dropped. Meanwhile, the avalanche crushes a nearby village. Using explosives, Harry successfully separates the last three cars before they are buried in the avalanche's path. The rest of the Express enters the safety of the tunnel.Disguised as Professor Heinz Golchak, Bunin checks into a Swiss hotel and meets with Geiger, the leader of a German terrorist cell. In exchange for providing Geiger's associates in hiding with an escape route via a Soviet freighter, Bunin wants the terrorist group to destroy the Atlantic Express, wearing their customary black uniforms and masks. That evening, after passing through tight security at the Zurich train station, Bunin boards the Atlantic Express in disguise, along with Geiger and Geiger's female associate, Helga Mann.In the morning, the Atlantic Express arrives in Maastricht, Holland, and Dutch intelligence officer Scholten goes on board to assist the Americans for the remaining journey. Scholten informs Harry that a Soviet freighter, The Maxim Gorky, is suspiciously lingering in the waters off the coast of Rotterdam, Holland. Meanwhile, Bunin notifies Geiger that one of his men planted weapons in the bathroom ceiling, located behind the engine room. Geiger collects the stash and distributes grenades to Bunin and Helga. As the train is nearing a river bridge, Helga opens the operator compartment and threatens to trigger the grenades if the train does not slow down. As the locomotive comes to a stop, the Geiger Group waiting in the adjacent meadow attacks with machine guns. Grabbing Helga, Leroy leaps overboard into the water, setting off her grenade away from the train. Bunin throws a grenade towards Marenkov's compartment, but the Soviet defector and Elsa escape the blast and jump off the train. Harry shoots Geiger dead and Scholten's men kill the remaining terrorists, but Bunin gets away on a motorboat standing by to take him to the freighter.Harry explains to Scholten the importance of intercepting The Maxim Gorky since it will not only provide refuge for Bunin, but also for valuable Soviet undercover agents. To deceive Bunin, Harry, Marenkov, Elsa and Scholten disguise themselves in the uniforms of the Geiger Group, and proceed to the freighter's location in a torpedo boat. As they approach, Bunin is surprised that these terrorists survived the train assault, but instead of picking them up, he orders the Soviet officers on the freighter to shoot. To counter the attack, Harry and his group fire torpedoes, setting off a series of explosions that destroy everyone on the ship including Bunin.Later, on a plane to the United States, Haller informs Marenkov that Bunin's death and the exposure of the Winter Harvest agenda has weakened the militant hawks in the Soviet government. Content, Marenkov hums a song on his way to a new life in America.