Later, aboard the train, Garrett tells Spencer what he saw the night Alison disappeared, namely seeing Byron and Alison's meeting in her backyard. Garrett also tells Spencer that that even though he didn't kill Ali, Jenna thinks he did.
While Spencer goes to find Aria so that Garrett can tell her what he saw the night of Ali's disappearance, Garrett is taken captive, although this takes place off-screen.
He is shot to death by Darren Wilden, who was working alone and dressed up as Queen of Hearts because he had discovered that the latter was a dirty cop and was going to tell. His body is locked inside a wooden crate, along with Aria. The box is almost thrown off the train by two unknown assailants (a female who sounded intent on throwing the box off the train and a male who was trying to dissuade her) but the girls arrive and pull it back inside the train at the last minute.
Melissa later reveals to Spencer that Wilden was taking order from someone (probably the new A) and Wilden, in turn, was giving orders to Melissa as well as to Jenna and Shana.
Melissa also reveals that she didn't know Spencer AND Aria (not Garrett) were the real target. She claims that Wilden saw Garrett with Spencer and planned to only kill Garrett. After Wilden killed Garrett, he attacked Spencer.
It is possible that Melissa was the Queen of Hearts who drugged Aria. It is also possible that Melissa didn't know Mona was on the train (and wearing an Ali mask) on Halloween but Spencer revealed it to her after Melissa explained everything her involvement in the events that took place aboard the train.