During one of the Cristina missions, Ezio follows Cristina in secret and finds her being cornered by Vieri who intimidates her, telling her he's 'tired of waiting for her to open her legs on her own' and attempts to assault her. However, the player will interrupt him and beat him up.
Maybe. In the mission Castello Crasher, Lucrezia Borgia hits Caterina Sforza pretty badly before leaving. In the mission, An Apple A Day, Cesare Borgia chokes Lucrezia Borgia so she'll tell him where the Apple of Eden is.
An attempted rape is prevented. Another character is held prisoner for a time, and is asked about rape, but denies it. A woman is hung after being assaulted by a corrupt executioner.
Yes, in the mission Castello Crasher, Lucrezia Borgia lightly tortures Caterina Sforza by hitting and heavily damaging her leg. She does it once before leaving.
There is no homophobia at all in this game (to my knowledge), Leonardo Da Vinci both in Assassin's Creed II and now in Assassin's Creed: Brotherhood is heavily implied to be gay, and in the DLC, the Da Vinci Disappearance, it's outright confirmed that he and his assistant Salai are together, which Ezio approves of.
Some of the melee moves trigger bone-breaking sounds. This can be minimized by sticking to bladed rather than blunt weapons, but I don't think it can be avoided entirely
Ezio can poison enemies, who will die after a short while. Both Rodrigo and Cesare Borgia poison each other, with Rodrigo dying because of it, and Cesare getting sick.
A major character in the modern day storyline is killed after it's revealed they were working for the Templars and were going to betray the cast at some point.
Kind of, most of the game takes place inside of the Animus, a machine that lets someone relive the memories of the ancestors. The player can be desynchronized if they die or fail a mission, the animus glitches rather frequently. Not to mention the whole precursor and Subject 16 stuff.
Yes, however that hanging itself isn't entirely shown, just the aftermath. Also in the second Cristina mission, Ezio gives last rites to his father, older, and younger brothers who were hung in Assassin's Creed II, however their hanging isn't shown again.
During an optional quest, the player has to eliminate a character named Lanz, who is said to kill people by pushing them off of buildings.
The player has the option to grab enemies and throw them off roofs and buildings or into the water, causing them to drown.
Bartolomeo's wife, Pantasilea gets kidnapped during one sequence, but eventually gets rescued by the player.
Caterina Sforza is captured by the Borgias but also saved by the player.
In the Da Vinci disappearance DLC, Leonardo is kidnapped and must be rescued.
Yes, *SPOILERS* at the end of the game, Desmond is possessed by Juno and is forced to stab and kill Lucy Stillman, however this is because *SPOILER AGAIN* Lucy is a Templar double agent.
Kind of, throughout the game, the player can hit NPC's with their horse. It doesn't kill anybody, but it does anger enemy NPC's. Also in the mission, Outgunned, Ezio can use the wagon to knock over enemies who chase him on horseback.
Yes, if an NPC ever goes into the water, they die. (The amount of times I have desynchronized because an NPC I had to protect fell in the water and died, is an angering amount)