Simon wasn't murdered. He had depression and he committed suicide.
Nate's locker had been searched at school and Simon's EpiPen and the EpiPen's that belonged to the nurse's office had been found inside. Nate is convicted of the murder and is arrested. Bronwyn, Addy, and Cooper further investigate the truth behind this murder because they suspect Nate isn't to blame.
Addy eventually finds out the truth behind Simon's death. She figures out that Simon hadn't been murdered and that unfortunately he planned his death himself. He was depressed and he wanted to get back at the four students for things that they have done to him.
Simon being depressed desperately wanted to be popular. He knew of Addy cheating on Jake, so he set up a plan for them. This is when he thought of commiting suicide and blaming the four for murder. Jake seemingly also wanted to continue Simon's plan because he wanted to avenge Addy for cheating on him. They involved Janae, Simon's best friend, and she was originally forced to put the EpiPens in Addy's locker, but she chose to put them in Nate's.
While Addy is at Janae's house, Jake finds Addy and attempts to hurt her. Cooper arrives at Janae's house and stops Jake from hurting Addy any further. The cops arrive and Jake is charged and arrested for assault and more reasons.
Jake is taken to jail and Nate is released. Bronwyn and Nate's relationship doesn't last any longer because Nate believes that he shouldn't be with her.
In the end, every one begins to find themselves and do their own things. Everyone gets themselves back together. Addy starts to enjoy running. Bronwyn applied to her dream school, Yale. Cooper is being accepted into colleges for baseball. Nate has ended his use with drugs and is now happy with his mom who has decided to stay home with him.