In a hospital in Tokyo, the movie begins. Yuichi Kimura/”The Father” (Andrew Koji) is by the bedside of his son Wataru (Kevin Akiyoshi Ching), who was thrown from a rooftop while his father was absent.

The Elder (Hiroyuki Sanada), Yuichi's father, arrives and explains to his son that dads are responsible for safeguarding their families. Yuichi sets out to find the person who injured his kid.

Brad Pitt's Ladybug, an assassin, is making a comeback from a leave of absence. Since he doesn't think he's lucky like ladybugs often are, he finds the name amusing. He is also standing in for sick Carver, another assassin.

Ladybug instructs him to board a bullet train traveling from Tokyo to Kyoto after speaking with his handler, Maria Beetle. He has to find a briefcase with money inside that has a train-themed sticker on the handle. Yuichi bumps into Ladybug as he approaches, causing him to drop his train ticket and a key to a locker. Maria insists that Ladybug take the gun when he discovers it after breaking into the locker.

"Twin" brothers and assassins Tangerine and Lemon are riding the train (Brian Tyree Henry). As his kid is a drug addict and cannot be trusted on his alone, a mafia lord known as "The White Death" dispatched them to find him. Lemon compares particular people to characters from "Thomas The Tank Engine" and bases much of his philosophy on the show.

Tangerine tells Lemon about White Death, a wandering Russian who ended up working as Minegishi's right-hand man as a Yakuza boss before starting his own gang, betraying Minegishi, and killing him. While keeping the Son company, the brothers argue about how many people they killed altogether (one was an innocent bystander in the wrong place at the wrong time).