Fujiko has stolen something from a man named Pycal, and he wants it back. Pycal is a magician who is able to shoot flames from his hands, walk on air, and deflect bullets with ease. Lupin goes up against Pycal in hopes of saving Fujiko. (Pycal first appeared in chapter 7: "Magician" of the original manga series.)

A boat collision ruins Lupin and Fujiko's quiet boating expedition. They discover a woman named Linda in the other boat just as gunmen on a larger boat attack them. After avoiding the gunboat, they learn that Linda is the assistant to a world-renowned expert on nuclear fission. She lived on an island with the doctor, which also housed the "Kirein Killers" ("Killers of the Sea"). Lupin and Jigen try to storm the island to save the Doctor and discover Linda's mysterious secret.

Lupin and Fujiko successfully pull off a heist; that is, until Zenigata manages to shoot Lupin with a tranquilizer dart. Zenigata hauls Lupin off to jail. Despite Fujiko's best efforts, she cannot break Lupin out of prison, and Jigen provides no help, claiming that Lupin can leave whenever he wants. One year passes, and Lupin's still in jail with his execution date getting closer. Fujiko and the others try to help Lupin get out of jail.

Goemon Ishikawa XIII is the thirteenth direct descendant of the famous samurai highwayman Ishikawa Goemon. Goemon's mentor has given him a mission; find Lupin and use the invincible Zantetsuken eliminate him. Neither Goemon nor Lupin know that Goemon's mentor and Fujiko are actually working together.

One rainy afternoon, a man seeks Lupin's help on behalf of a young woman. The woman is actually Fujiko, who is after a diamond known as "The Star of Killamanjaro". The diamond was implanted into the chest of a mob boss. This boss had his memory wiped but died days before it was to be restored. Now, Lupin and the gang are after the ambulance carrying the corpse and the diamond in it. Zenigata is in charge of the ambulance and its escort, and he attempts to prevent Lupin from stealing the diamond.

Three scrolls contain the secret of creating a blade like the Zantetsuken. Lupin wants to steal them as a matter of family pride because his grandfather, Arsene Lupin, stole them back in the 19th century. Lupin's father stole a dagger from a swordsman that was forged using the same process. The swordsman challenged Lupin II to a duel and lost. But, he managed to steal the scrolls for himself. Now, Lupin plans to steal the scrolls back, but to do so, he must face Goemon and Fujiko, who have their own plans for acquiring the scrolls.

Napoleon once owned a deck of fortune-telling cards that are now in the hands of a millionaire known as Mr. Gold. Lupin plans to steal them during Mr. Gold's birthday party, and Zenigata plans to stop him. Lupin succeeds in stealing the mysterious cards.

Lupin and the gang aim to steal the blue prints for a new computer. In their way is a man skilled with the machinegun and his hit-man partner named Poon, who used to be Fujiko's partner in the past. Lupin succeeds at his mission, but not before Poon and Fujiko come face to face. Poon's boss shoots Fujiko before they can have a proper reunion. Lupin manages to get Fujiko back to their hideout, but she is near death. Poon and his boss follow Lupin and manage to oust him from the hideout, which leaves the dying Fujiko inside. Lupin tries to get back to the hideout to save Fujiko's life.

Lupin and Baron Ukraine are both after the world's most skilled counterfeiter. Lupin would have no problem beating the Baron, but the Baron has hired a man called Flinch along with Fujiko and gave them instructions to kill Lupin.