What we see in episode 1
Tommy Crane, Neagley's childhood friend, strips off on Chicago's elevated train tracks and walks into an oncoming train. Police lean toward an accident. Neagley doesn't buy it, because Tommy left her a message that only she could understand.
Why he was at Echo Canyon
Tommy went to Echo Canyon Farm, a commune with a cult-like feel run by Lawrence Cole, looking for help with old trauma. He was hoping the farm could take it away.
What he found
Echo Canyon was a front. Underneath, there was a secret testing ground where an experimental drug called Tranqlara was being tried on vulnerable people. Tommy started digging into what was really going on there.
Who ordered his death
In episode 3, Neagley gets confirmation that Cole had Tommy murdered. Cole works with drug company CEO Pierce Woodrow, and above both of them sits a wealthy Scandinavian businessman, Arvid Rawlings.
The connection to Neagley's past
Tommy was abused as a child by a man named Elliot Percy. Neagley's father, Calvin, killed Percy, and young Frances saw it happen. That is why Neagley's own past is tied up in the case. Her father told her that nobody would ever touch her again.
Does anyone pay for it?
The finale doesn't leave it hanging. Neagley doses Rawlings with the same drug, and he wanders into traffic much the way Tommy walked into the train. Cole appears to die when the silo beneath Echo Canyon is destroyed. Woodrow was killed by Rawlings back in episode 7.
For the full ending, see Neagley season 1 ending explained.