Instances of rape in this comic: five.
First instance. Kirihito's fiancée Izumi is raped by his colleague (and best friend?) Urabe. Izumi tells Kirihito she wants to get married straight away, because she's worried she "might stray", and that Urabe's looks make her uncomfortable. "I don't like him one bit" she says, "but he comes on so forcefully. And you're so cool towards me". A married woman is safe from sexual predators, but unmarried ones are fair game. What's particularly twisted is that Izumi uses language that puts the blame for her impending assault on herself: she "might stray".
Second instance. Kirihito and his wife Tazu are running away together. When travelling in a forest, Tazu goes off to get some water and a stranger tackles her to the ground. When Kirihito finds her, she has been raped and killed by the stranger, who flees. The stranger then makes very minor impressions on the rest of the book's plot until he is discovered by Kirihito at the end, who hands him over to a priest. The rapist is therefore little more than a means to deprive Kirihito of his wife in a disturbing but sensational way.
Third instance. Kirihito is tied up and raped by a circus performer called Reika, who has ensnared and killed seven other men in a lonely cabin in the mountains. She has a "fetish for freaks" and an "abnormal libido". Kirihito treats this as a medical rather than a moral issue. He decides it is caused by the stress of performing dangerous stunts, and tries to cure her using hypnosis. Although Reika has sexually assaulted him several times, they remain amiable and continue their travels together, although Kirihito remains loyal to Izumi and Tazu. Reika considers prostituting herself when they have no money, and finally dies in the attempt to earn enough to get Kirihito back to Japan.
Fourth instance. Although Izumi has been raped by Urabe, she goes to him to ask about Kirihito's fate and they conspire to find him. Her rape hasn't poisoned their relationship, although when Urabe confesses that he loves her and kisses her, she smacks him away. Izumi's parents suggest that she marries Urabe now that Kirihito is presumed dead, and Izumi (more from loyalty to her fiancé rather than disgust at Urabe) tries to commit suicide. Urabe is distraught and rapes one of his patients, a nun called Helen Friese. Friese seeks sanctuary in a church, but Urabe finds her, apologises, says he loves her and wants to cure her. They are reconciled in a silent panel which highlights a hanging figure of Jesus on the cross. Urabe is forgiven by both his victims.
Fifth instance. Izumi's parents work for Urabe's boss, and when he is fired (meaning he can no longer see Friese), he takes his revenge by raping Izumi a second time. When he commits suicide, Izumi's reaction isn't shown, but Friese mourns for him.
Justifiable depictions of rape in this comic: zero