Mona's kidnapper was an anonymous character that was revealed to have been Charlotte DiLaurentis as A in Game Over, Charles. At the end of Taking This One to the Grave, viewers were lead to believe this person was Mona's killer. The character has blonde hair that may or may not be a wig and appears to be brutal as the Vanderwaal household is in shambles and blood stains are left all over the place, though it is later revealed that Mona splattered blood on the walls in an attempt to fake her death.
At first, some people believed there was a hair/wig change between the scenes, implying that there may were two people breaking in. But after 'A' was revealed to be Charlotte DiLaurentis, we can assume it was just her hair this whole time. It was revealed in Pretty Isn't the Point that Mona and 'A' were going to fake her death and blame it on Alison; however, Mona planned to double cross 'A' and get answers on their identity, then come back to town and free Alison, becoming a hero. It was believed that 'A' double crossed Mona and killed her for real, but in Welcome to the Dollhouse it is revealed that Mona is alive and was being held captive by 'A'.
In Taking This One to the Grave, we see someone with blonde hair that looks like Alison's breaking into Mona's house, going up the stairs. After that, we see another anonymous person, but with straight blonde hair going into Mona's bedroom and Mona sees the anonymous person.
In Through a Glass, Darkly, a hidden camera is found showing a part of the fight between Mona and the anonymous attacker who got into her room. The attacker appears to push her down the stairs, jump down and try to kill her.
The murderer put Mona's body in a trunk.
Spencer mentions in Through a Glass, Darkly that there were traces of Mona's DNA in Alison's trunk and Carla Grunwald says she feel Mona is surrounded by earth, insects and cold and is not having an easy passing. In this episode, Alison is being arrested and put in jail for Mona's murder, the girls are not so sure that Alison killed Mona after A keeps terrorizing them while Ali is in jail.
In Pretty isn't the Point, we find out that Mona and Big A were planning to fake Mona's death so that Ali would be locked up. Mona planned to come back to Rosewood after she finds out who A is so that the girls will be safe and Ali will be out of jail. She took her own blood and that is probably the reason she fainted in A Dark Ali. She was supposed to meet Mike Montgomery a few times but she never showed up. Mike thinks A double-crossed Mona and killed her.
In Welcome to the Dollhouse, it is revealed that Mona was never murdered and is being held captive in A's dollhouse. The attacker never tried to kill her, they were trying to drug her and take her to the dollhouse. However, the reason that the assailant entered Mona's home and kidnapped her remains unknown.
- Marlene King said on Twitter that 'A' attacked Mona in her home and then kidnapped her whilst wearing a balaclava and took her to the dollhouse. Supposedly, 'A' then spread the blood Mona had been storing around her house to make it look like she had been murdered.