The story takes place in France during World War II, and is about the mercenary Pip Bernadotte, as he joins the resistance against the Nazi occupation. The Nazi soldiers controlling the region have made themselves unpopular by oppressing the people and raping women, attracting many people to join the resistance. Walking through the streets of the town, Pip sees a young woman who, although not a prostitute by all appearances, asks him to buy her for the night. Rather confused, he spends the night with her, and she leaves in the morning without demanding any money. As it turns out, she is the daughter of the governor, who had been killed by the occupation, and she is soon captured by Nazi police and taken to the commanding officer's mansion, where she is brutally raped. Pip and the resistance storm the mansion and rescue her, fleeing before reinforcements arrive.
Afterwards, following the injury and probable death of the commanding officer during the battle, the Nazi High Command appoints SS-Sturmbannführer Montana Max to rule over the region. Another newly-appointed officer, upon entering Max's office, is shocked to see that Max allows his soldiers to copulate with captured women within the office, whereupon Max explains the story of his childhood and says he has no feelings about it, only disconcerting the officer further. When he was young, Max lived in a single room with his alcoholic father and his prostitute mother, who received clients directly in the family's single room. After his father's death and his mother's indifference to it (she received a client that very same day), Max retrieved his family's pistol and killed his mother and her client, after which he wandered alone in the streets before being noticed by the Führer and raised to a high office of power. This is where Max's indifference to all things including sex, and his love of cold-blooded killing stems from.
Pip and the other resistance members again storm the mansion, wanting to kill Montana Max, only to find that he had guessed their plans and had taken an airship to South America, a place where many Nazi officials fled during the end of World War II. Following him to South America, one of the resistance leaders (the Coyote) is assassinated by undercover agents, and Montana Max fails to be found. As Pip and company sail back over the sea, the last line reads, "Coyote may be dead, but another day some other coyotes will return to hunt their prey."
Connection to Hellsing
In the creation of Hellsing, his most acclaimed work, Kouta Hirano pulled motifs from many of his earlier manga, and many similarities can be noted. A character named Pip Bernadotte appears in Hellsing, bearing many similarities to his Coyote namesake. Still, considering that Hellsing takes place 56 years later and Pip's age is hardly different, it is most likely non-canon to Hellsing. However, it's sometimes assumed by fans that it was Pip's father or grandfather in the manga, although there is no information that confirms this. Additionally, The Major, the villain of Hellsing, appears in his early prototype incarnation here as "Montana Max". Several other Hellsing character prototypes can be spotted in Coyote, including a woman who resembles Yumie/Yumiko from Hellsing and Crossfire, as well as a primary character in Hi-and-Low.