With Last Supper already in disrepair, in 1652 monastery residents cut a door into the middle of the painting, removing Jesus’ feet and creating the large gray space seen in the bottom of photos of the painting. Later in the 1700s, soldiers of Napoleon Bonaparte turned the refectory into a stable and used the painting as target practice for projectiles. During World War II, the Nazis bombed the monastery, but the painting was luckily protected by sandbags so was not completely destroyed. However, all of this clearly did not help the already-flaking painting.

Sources:

The Last Supper – by Leonardo da Vinci. (2011). Retrieved from https://www.leonardodavinci.net/the-last-supper.jsp

Issacson, W. (2017). The Last Supper. In Issacson, W, Leonardo da Vinci. (pp. 273-292). New York, NY: Simon & Schuster