Tsukigasa

A one-volume manga set in the Samurai era, Tsukigasa begins with a man with suspicious injuries showing up at Azuma's clinic. Azuma and Tatsumi quickly realize it's their old friend, Kuroe, who left 5 years ago after a sexual encounter which ended in Azuma cutting Kuroe's left arm off. It transpires that Kuroe was picked up by robbers after he left, and Tatsumi intends to arrest him. Azuma refuses to let Kuroe leave until he is healed and the trio spend a tense few days together.

The robbers eventually catch up to Kuroe, who reveals to Tatsumi that he was only a healer for the syndicate and was injured trying to run away with sensitive information when he found out their next target was Azuma. When they arrive at the clinic Kuroe dispatches them quickly, and Tatsumi pulls some strings to get him cleared.

Kuroe and Azuma try to resolve their issues from the past, but fail until Toubee, Kuroe's father and Azuma's teacher, comes back and angrily chastises his son. Azuma overrides him and accepts responsibility for everything that happened, finally making his true feelings towards Kuroe clear. They become lovers and to Kuroe's surprise even Toubee forgives him for leaving, restoring back to him the idyllic life of five years ago.

Tropes used in Tsukigasa include:

Bishonen: Azuma is none too happy about being treated like a girl because of his looks. Particularly because he was raped due to his resemblance to his mother.
Broken Bird: Kuroe goes from idealistic to pure cynicism after the person he loves cuts his arm off and he runs away from home, ends up in a ditch, and is saved by robbers (whom he hates).
Cannot Spit It Out: Kuroe and Azuma in regards to their feelings.
Can't Hold His Liquor: Kuroe is drinking his father's sake while he's gone and dares the 16 year old Azuma to try it too. It turns out he's a total lightweight and an affectionate drunk, which takes a turn for the worse when this leads to sex and the extremely drunk Azuma calls up some trauma from his past, hallucinates that Kuroe is his rapist uncle, and grabs a sword and cuts Kuroe's arm off.
Creepy Uncle: Azuma's uncle rapes him after Azuma's mother (his uncle's sister) dies because he resembles her.
Empty Nest: Tatsumi actually uses this to describe how he feels now that his two friends are together and caught up in their relationship. Considering he was the Team Dad, it makes sense.
Fainting: Azuma does the emotional variant of fainting when Kuroe killing the robbers brings up trauma from when he hurt Kuroe.
The Farmer and the Viper: From the robber's perspective Kuroe's betrayal is like this, although they weren't innocent people to begin with.
Guilt Ridden Accomplice: While Kuroe never approved of thievery the robbers were surprised when he tried to make off with their maps, and Tatsumi was surprised when he gave them to him to help arrest the criminals and Kuroe still wanted to turn himself in too. Ultimately it comes down to Kuroe being a righteous sort of person and wanting to protect Azuma as well.
Handicapped Badass: Kuroe has no trouble killing the robbers even though he only has one arm.
Hates Being Touched: Azuma can't stand contact from other people ever since he was raped by his uncle.
Heroic BSOD: Azuma has one after cutting off Kuroe's arm, being Driven to Suicide at one point.
Inter Class Romance: Azuma's family is loaded, whereas Kuroe is of slightly more modest background (still a doctor though).
Long-Haired Pretty Boy: Azuma.
Maybe Ever After: Tatsumi, who feels rather left out after Kuroe and Azuma hook up, gets a potential Love Interest in the extras, with the restaurant owner.
May-December Romance: The significantly older Toubee and his 18 year old pregnant fiancee. Even his own son is older than her.
Missing Mom: Azuma's mother's death is what sparked the rape incident.
My God, What Have I Done?: Azuma, having a drunken illusion of Kuroe being his rapist uncle, cuts Kuroe's arm off. He goes into Heroic BSOD mode almost immediately.
Must Make Amends: Azuma feels incredibly guilty about cutting off Kuroe's arm, but doesn't know how to make amends. Eventually he gives Kuroe a blade and tells him to do whatever he likes. This still doesn't solve the problem and it's only when they finally are completely honest about everything that it gets resolved.
One Side of the Story: Everyone has one side of the story and they refuse to just put it all out in the open. Eventually all the pieces are dragged out, one by one, and things are resolved.
Pint-Sized Powerhouse: Azuma is capable of beating up 5 guys in a fight and leaving them with broken bones. His skill is part of why the damage is so extreme when he attacks Kuroe later, cutting off his left arm in one strike.
Poor Communication Kills: Nobody remotely discussed what exactly happened in the arm-cutting incident or their feelings leading to everyone having a completely different idea of what went on and who regretted what. When Kuroe comes back it still takes them a long time to finally come out with the truth. Kuroe also is nearly arrested by Tatsumi because he was too proud to reveal he wasn't actively a criminal.
Precocious Crush: One of Azuma's students tries to disrupt Kuroe's lessons because he has a crush on Azuma and sees Kuroe as his rival.
Rape as Backstory/Rape as Drama: Azuma being raped by his uncle provides explanation both for why he Hates Being Touched, and why he freaks out like he does when Kuroe makes advances on him.
Samurai: Tatsumi is a Tokugawa-era one, and thus more of a public officer than a warrior.
Shotgun Wedding: In the extra it's mentioned Toubee will be marrying an 18 year old girl because he got her pregnant. Everyone's rather shocked.
Stockholm Syndrome: Subverted. Kuroe was known to have joined a robber syndicate after they saved his life and so everyone assumes he became a criminal by choice due to this. In truth he never actually approves of them and only acts as their doctor and when he finds out their next target is Azuma, he steals some very important maps, runs off, kills the men who come after him, and gives all the information to his Samurai friend so he can catch the rest of them. His gratitude really did have its limits.
Tender Tears: Azuma. They are somewhat comical considering his stated goal is to become more manly.
Tsundere: Kuroe flips between hot and cold with Azuma when they reunite, sending mixed message after mixed message.
UST: Azuma and Kuroe have five years of it to resolve.
"Well Done, Son" Guy: Kuroe starts crying when his dad unexpectedly forgives him for running away.