- The game lets you know quite early on that it will be a very sad story when Amicia loses her poor dog Lion, who has been wounded by the rats while chasing a boar. Moments after finding him, she watches with horror as Lion is dragged underground.
- Later, if the player chooses to do so, she offers a prayer for poor Leon at the chapel inside her home.
- Roughly an hour later, after Amicia has made contact with her brother Hugo, she watches from a window as Sir Nicholas cuts down her father Robert.
- Amicia and Hugo must then creep by, helpless to do anything, as Inquisition forces proceed to murder all the servants in the De Rune estate. The children are later separated from their mother when she is forced to stay behind and fend off Nicholas.
- In Chapter 2, Amicia is forced to battle a former solider named Conrad by knocking off pieces of his armour with her sling. She begs him to stop, but the grieving Conrad presses on, clearly expressing his wish to die so that he can be with his deceased family. Amicia is finally forced to kill him, an act that causes her considerable guilt, and for which she prays forgiveness for.
- In Chapter 4, Amicia and Hugo finally reach the farm of the alchemist Laurentis, who is dying of the plague. Lucas, who is Laurentis' apprentice, helps them escape the farm after it is overwhelmed by rats, but not before he watches as Laurentis' farmhouse goes up in flames with the alchemist still inside.
- In Chapter 9, Amicia stumbles upon an area of a French town that is filled with the corpses of townsfolk who became sick and were slaughtered by the Inquisition. Some of the townsfolk are still alive but dying, including one man who begs Amicia for water before collapsing by a stream choked with corpses.
- In Chapter 12, Amicia returns to the De Rune Estate to find it completely overrun by the rats. She finds the body of her father, strangely untouched ... until the rats swarm together and attack Amicia, at which point they seem to carry Robert off.
- Amicia and Lucas find the bodies of several servants throughout the estate, including one man who had died protecting her mother Beatrice.
- In Chapter 13, Hugo runs off after learning Beatrice is still alive. Amicia is injured while searching for him and is tormented by visions of others chastising her for her failures and the ghosts of the men she has been forced to kill.
- In Chapter 14, Hugo sneaks through the headquarters of the Inquisition. At one point, he finds a man in a cell who begs Hugo to free him, but there is nothing he can do.
- Hugo is later forced to kill for the first time (with the help of the rats) when Grand Inquisitor Vitalis tries to push him past the first threshold by ordering soldiers to attack Beatrice.
- In Chapter 15, Sir Nicholas attacks the orphans' home base of Chateau D'Ombrage. Nicholas murders Melie's brother Arthur before Amicia and Hugo are able to defeat him.
- In Chapter 16, Rodrik sacrifices himself by pushing a carriage that shields Amicia and Hugo from archers but not him. He is peppered with arrows and dies seconds after getting Hugo and Amicia to safety.
- Earlier in the chapter, Amicia may discover the forge where Rodrik worked with his father. Rodrik collapses to his knees after finding it has been swallowed up by the rats' corruption in much the same way as the De Rune estate.
Tear Jerker / A Plague Tale: Innocence