Alison FitzLaurentis Theory: Could Alison DiLaurentis and Ezra Fitz be RELATED on Pretty Little Liars?!
What if Ali is secretly EZRA'S YOUNGER SISTER?! Recall that in season 1, EZRA TOLD ARIA in season 1 that his parents had cheated on each other but in the end it wasn't their infidelity that tore them apart. Ezra wondered if Aria's parents had an "arrangement" similar to his parents' situation. Maybe Ezra's father cheated on Creepy Diane "FitzScary" with Jessica DiLaurentis. Perhaps they had a differing of opinion when it came to how Alison would be raised. Maybe THAT is what tore them apart.
Perhaps Ezra JUST RECENTLY found out about all of this. The MAGGIE/MALCOLM story seems pointless now that Malcolm isn't Ezra's son -- unless he found out OTHER information when getting his DNA tested. Ezra jumped at morphing into a father figure when he found out about Malcolm being his "son." He's the type of guy that would set out to find his sister immediately upon learning that he had a sister. He could have done exactly that; He could have realized exactly who the sister was (Alison), then FIGURED OUT that Ali was ALIVE but had to KEEP IT FROM ARIA because he also discovered that somebody was out to get Alison and would have no problem taking down her friends to do it. Next, he created the lair to SPY ON THE GIRLS so that he could have excuses for/ WAYS OF randomly showing up just in time to save the day (Halloween episodes "This is a Dark Ride," and "The Grave Truth," for example. In "This is a Dark Ride," Ezra claimed that he went to the end of the line to surprise Aria, but HE was the one who seemed shocked. Maybe that's because he saw Aria get drugged and put in the box from the lair, RUSHED to get there, but since he couldn't monitor what was happening during his drive, assumed the worst: that Aria got hurt or killed.
In "The Grave Truth," he just happened to call Aria right when the girls got to the cemetery (which he likely knew they were going to b/c of the lair), warn her to be careful, THEN show up to drive the girls home when Spencer had a flat tire. As if that's not enough, right when Alison was spilling that she was afraid of somebody dangerous, she suddenly made the "shhh" signal and disappeared RIGHT WHEN Ezra showed up because "Aria forgot her phone."