The killer followed Charlotte to The Church and engaged her in a violent fight. In the end, Charlotte was killed with a something hollow with a rectangular shape, later revealed to be a staple. Afterwards, the killer cleaned her nails to get rid of any DNA and threw the body off the bell tower to make it look like a suicide.
In "Tick Tock, Bitches", the Liars think that Alison killed Charlotte. At Alison's house, Emily found the red sweater that belonged to the blonde woman who was seen by Aria and Ezra entering the church that night. It was revealed in "Hit and Run, Run, Run" that the Red Sweater Blonde was Ali, but she didn't kill Charlotte.
In "Farewell, My Lovely", Mona reveals herself as the killer. She met Charlotte at the the church's bell tower in an attempt to stop her from continuing the game. Mona tried to scare her by pinning her at the window of the tower, seemingly about to throw her off, but backed off. They engaged into a fight where Mona accidentally killed Charlotte in self-defense, by throwing her against a staple.
- In "Tick-Tock, Bitches", The Liars along with Ezra, Toby and Caleb secretly voted for the identity of Charlotte's killer. We can presume the votes were:
- Alison: 4 votes (possibly from Aria, Ezra, Toby, and Caleb)
- Mona: 1 vote (possibly from Spencer)
- Spencer: 1 vote (possibly from Mona)
- "No name": 1 vote (from Emily, who also thought Alison killed Charlotte, but had doubts about it.)