I just finished re-watching season one of “Pretty Little Liars” and came up with a theory explaining Ian`s behavior.
Ian knew EVERYTHING. Melissa told him she buried “Alison`s” body to keep Spencer out of trouble (now we all know that Melissa actually buried Bethany, not Alison). Ian also knew that Alison was alive.
After Ian and Melissa get married, the liars are still convinced that Ian killed Alison. Ian is annoyed with Spencer for trying to pin Alison`s murder on him. His conscience is clear though, because he knows that Ali is alive but he can`t say anything. This might have to do with the secret videos he probably thinks she has. Ali might be threatening him, saying that she`ll reveal the videos if he tells anyone that she is alive.
'A' (Mona) plants a trophy with blood on it and makes the liars believe that it belongs to Ian and that he used it to kill Alison. First 'A' makes Toby look guilty. Then Noel. Now it`s Ian`s turn. It`s all a part of 'A`s” (Mona`s) game to torture the girls. The liars run with this theory and bring the trophy to the police. As it turns out, the blood belongs to a rat, not a person. 'A' set the liars up. Ian realizes that Spencer won`t drop her suspicions. She will never let him and Melissa live in peace.
After things blow over, Ian and Spencer have a conversation. Ian tells Spencer something along the lines of “if you don`t take my advice and drop this, the police will come for you and then it will be too late.” This is a threat. Even though Ian knows that Ali is alive, Melissa and everyone else think that she`s dead. If Ian goes to the police and tells them what Melissa told him (how Spencer supposedly killed Alison), taking Melissa out of the equation of course, since he doesn`t want the mother of his unborn child to go to jail, Spencer will be arrested. She will no longer make Ian`s life difficult by asking questions about Ali and accusing him.
The flash drive with the secret videos (most likely filmed by Ian) the girls find in Alison`s old lunch box could do a lot of damage to him, Jenna, and probably the whole NAT club. The liars decide to trap Ian by sending him a text and ask for money in exchange for the flash drive. In their minds, if he wants to get the videos back and agrees to pay up - he killed Ali. If he doesn`t, then he probably didn`t. Ian agrees to meet and make the exchange. At this time he doesn`t know that he`s communicating with Spencer and her friends .
Conveniently enough, Jenna gives Ian a call and tells him that Spencer and her friends are ones who have the flash drive. Ian realizes that this is a set up. He decides to end this game once and for all. He sends a random guy to hand over the money and heads to the church to find Spencer.
When Spencer comes to the church to look for Melissa`s cellphone (since she left it there), Ian is already there. Mrs. Hastings probably told him that Spencer is there. He chases Spencer up to the bell tower and is clearly ready to kill her. Spencer tells him “If you love my sister, you won`t kill me.” Ian says that he WILL kill Spencer, BECAUSE he loves Melissa.
This sentence makes a lot more sense now that we`re half way through season 5. Melissa honestly believed that her sister killed Ali. She buried the body and decided to keep it a secret but it was weighing down on her. Melissa had a miscarriage in the past and Ian was worried that the stress would lead to another one. He also knew that Ali was alive and who knows, someday she might want to “come back from the dead.” With Alison alive, the police would start looking into the identity of the person buried in Alison`s place. Maybe they would connect her death to Melissa. Ian didn`t want to take that chance.
He would kill Spencer and tie up all the loose ends. He would tell Melissa that Spencer tried to kill him just like she “killed” Alison. Melissa would believe himbecause at this point she still thinks that Spencer is capable of murder.
But just as Spencer is about to fall to her death, black hoodie (Alison) shows up. Ian recognizes Alison and says “What are you doing here?”He`s not surprised to see Alison alive, he`s simply surprised to see Alison at the church! Alison pushes Ian down and saves Spencer. She does this partly because she doesn`t want Spencer to die and partly because Ian knows that she`s alive and she doesn`t want anyone else finding out. In this case, “two can keep a secret if one of them is dead.”
Ian`s body is gone when the police shows up but it reappears in season 2. In season 5, Alison tells the girls that Ian wasn`t dead when she left the church. That is probably true. However, I think that she might`ve hired Cyrus to do the dirty work. Cyrus freed Ian, who was dangling in the air only held up by ropes, and later made sure that Ian turned up dead. Cyrus and Ali do share some kind of a past and she did say that if people found out their secrets, both of them would be in a lot of trouble. This might`ve been one of those secrets.
'A' (Mona) finds out about Ian`s death and uses the opportunity to mess with Spencer and Melissa by sending them fake text messages from Ian. That is why both Melissa and Spencer believe that Ian is still alive. Eventually, Ian`s body is discovered.