Mrs. Dilaurentis told Alison that Cece Drake was pretending to be her in Radley – I think she met Bethany there, and pretended to be friends with her (she probably knew about Mrs. Dilaurentis affair with her father, and wanted to know more.) Bethany thought they were really close, so she told Cece about Marion (possibly that Mrs. Dilaurentis killed her, or watched.)

Bethany then found out about the affair and how Mrs. Dilaurentis was lying to her, and then asked if her daughter was also lying to her. She eventually figured out that Cece wasn’t really Alison and just pretended to be friends with her.

Bethany runs away from Radley to find Mrs. Dilaurentis and Cece. When she sees Alison from behind, she thinks it’s Cece and attacks her. Mrs. Dilaurentis sees this but has to bury her and keep it a secret, or else Bethany would tell everyone the truth about Marion.

Cece, who sees this from afar, finds Bethany and hits her with the shovel. She starts digging the grave, but before she can put Bethany in there, she hears someone coming and runs. It’s Melissa, who finds the body, and thinking Spencer killed Alison, buries the body.

One year later, the body is found. Mrs. Dilaurentis is asked to identify the body, but she realizes it’s not Alison – she doesn’t say anything to keep her secrets, realizing that someone else killed Bethany. She realizes that it was Cece, but Cece makes her stay quiet because Bethany told her about Marion.

After she is caught by the police, accused of killing Wilden, she tells Holbrook that she knows who killed the girl. She uses the excuse Mrs. Dilaurentis told Mr. Hastings, that Spencer fought with Alison that night, and says she did it – that’s why Holbrook seems so invested in this theory later on, even using Alison’s polygraph confession to gather evidence for it.

Holbrook tells Mr. and Mrs. Hastings that Cece ran away, and knocked a police officer down. I think she ran away to make sure Mrs. Dilaurentis wouldn’t tell the truth – but she then finds out that that’s exactly what she was planning on doing, so she kills her. Alison told her she was leaving for Paris that night, so she goes to NYC and convinces her to give her the ticket and her passport, so she can escape.

Back to the day she disappeared:

She had been planning on running away for a while now, telling Spencer about her diaries so she be the leader when she’s gone, blackmailing people for money, figuring out her new identity. She was coming back home to get her stuff and run away when she was attacked. Alison manages to get out of the grave, with Mrs. Grunwald’s help - but she runs away before getting in the hospital.

After she leaves Grunwald’s car, she goes back home to finish what she started (Mona never confessed to seeing Alison that night, so it could all be a lie she told the girls.) When she gets there, she sees Cece killing Bethany, and decides that it’s the perfect opportunity for her to pretend she’s dead.

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So rounding up:

Bethany hit Alison thinking it was Cece

Mrs. Dilaurentis buried Alison

Cece hit Bethany

Melissa buried Bethany thinking Spencer killed her

Alison never saw Mona that night, and used Bethany’s death to pretend she was dead