During an attack led by Tower Tom's goons, Lily was captured and brought back to Beantown Brewery. Low on food, Tower Tom began using her to blackmail her sister into giving them supplies. When Lily finally managed to free herself of her bonds, she was accidentally killed by Tom. Tower Tom began forging letters from Lily to Red in an attempt to hide this and continue extorting Red for food.
Lily's body cannot be found in the Beantown Brewery due to Tower Tom having hid her body in one of the inaccessible vats, as he stated within the Beantown Brewery terminal entries. Using no-clip commands to access the vats reveals, expectedly, no set of remains, as this area was never meant to be seen.
Lily Tourette is mentioned only in Fallout 4.