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The short answer
Recaps and Wikipedia say Lawrence Cole ordered the killing of Tommy Crane. The hired killer Davos says so in episode 3, and in the finale Neagley tells Cole he killed Tommy. Pierce Woodrow and Arvid Rawlings are responsible for the Tranqlara operation that Tommy threatened. Reported
None of the episode transcripts or recaps we read shows who gave Tommy the drug. NME and TV Insider name no individual who gave it. They say Tommy was killed before he could expose what was happening, and Primetimer blames a network financed by Rawlings and managed by Woodrow. Reported
The night he died
Episode 1 opens at 2 a.m. in Chicago. TV Insider says a dazed man strips and walks toward an oncoming train. The man is Tommy Crane, Neagley’s childhood best friend, whom she treated as a brother. She hears of his death in a call from his mother, Tina. Reported
The episode 1 synopsis, as copied on fan sites, says police are ready to label the death an “apparent accident”. Mr. Crane says the conductor told police Tommy was so high he walked into the train. In episode 4 a man named Davis tells Hudson it looks like a man got high and walked into a train. Reported
Most coverage describes the apparent explanation as a drug-related suicide, and The Guardian calls it Tommy’s “apparent suicide”. Primetimer goes further and says police ruled it a suicide, but no source quotes police, so we do not say that. Hudson Riley says early on that it did not sound like an accident. Reported
The clues Neagley follows
Cameras and footage. The cameras around the train station were broken. Wider footage shows a young man, later named Keno, running from the area less than a minute after Tommy was hit. Keno is a witness. He says he was there on an unrelated job and saw a truck switch on its headlights and race toward him. Reported
Renee Birdwhistle traces someone who asked about repairs to the nearby camera, under a fake name and ID, to Charlie Hall, spelled Halle in a transcript. He turns up dead in his trailer, and Neagley and Hudson see a staged suicide. Reported
Buckwheat. Neagley finds buckwheat at the scene and links it to Echo Canyon, which grows it. Confirmed
The Lake Laverne Summer Camp clue. TV Insider says Tommy’s last letter compares Echo Canyon to Lake Laverne Summer Camp, a place Neagley knows he hated, and she reads the line as a signal. Dialogue and a recap spell the camp “Lavern”. A recap says no journal is among his belongings. Reported
Rye flour. His second message is an envelope of powder that reaches Neagley through her father’s house. The lab says it is rye flour. Episode 2 dialogue, in a fan transcript, says it was postmarked the day before he died, and recaps say that in episode 3 Keno finds the barn basement full of it. Reported
How the drug fits
TV Insider says Woodrow pitches Tranqlara in episode 1 as a psychedelic miracle drug that can significantly reduce depression and anxiety. A transcript has Neagley saying Tommy had no history of drug use yet had taken a large amount of psychedelics. Reported
Episode 5 makes the link. Neagley is secretly dosed with Tranqlara. Afterwards she tells Hudson the headlights felt like they were pulling her in, as they did Tommy. Reported
Primetimer says the drug’s hallucinations led Tommy in front of the train, and NME says he was killed through the drug. In the finale Neagley injects Rawlings with Tranqlara, and he strips, walks into traffic and is hit by a truck. Primetimer calls his end very similar to Tommy’s. Reported
None of the transcripts or recaps we read shows who gave Tommy the drug or how. One fan wiki names a person and a method, but no other source backs it, so we leave it out. Reported
Who gave the order
Episode 3 holds the key scene. Davos, wounded and sedated, is asked whether Cole had Tommy killed, and he says yes. Wikipedia summarises it as Cole ordering the death. Davos does not clearly say he did it himself and gives no reason. Within minutes a corrupt officer shoots him dead. Reported
Other scenes may point the same way. In an episode 2 scene a line says “he asks too many questions” and Lawrence answers “not for long”. The Review Geek reads it as Cole deciding to have Tommy taken care of. A recording Neagley planted on a dead driver captures a man saying Lawrence wants confirmation they got them all, which ties Cole’s men to the cleanup after the truck crash, not directly to Tommy’s death. Reported
In the finale Cole blames Woodrow and Rawlings. Neagley says he did not care about Tommy, Cole says he barely knew the kid, and she says he killed him. Reported
TV Insider, NME and Entertainment Weekly agree on the roles: Woodrow develops Tranqlara, Rawlings finances it, and Cole runs the commune that supplies test subjects. Primetimer puts the killing on a network financed by Rawlings and managed by Woodrow. Our reading is that Cole gave the order and the other two are responsible for the operation. No source shows Woodrow or Rawlings ordering Tommy’s death in particular. The chain is set out in who created and funded Tranqlara. Interpretation
Where Elliot Percy fits
Elliot Percy did not kill Tommy. He is the predator who abused Tommy as a child, and Neagley’s father Calvin, then a police officer, killed him years before the story begins. Confirmed
Recaps say Tommy’s parents had made Calvin promise never to tell. The finale explains why Tommy went to Echo Canyon: he was trying to heal. Neagley spots a Bernadette Bunny children’s book on his shelf, the kind Percy gave him, and realises what it means. Reported
Neagley saw her father kill Percy as a child, which also links to her fear of touch. Confirmed
Why he was killed
TV Insider and NME agree on the motive: Tommy found out what was going on at Echo Canyon, and the people behind it killed him to stop him exposing it. Confirmed
An episode 2 flashback, two weeks before his death, shows what he saw. He tells a girl at the farm, Lulu on the fan wiki, that no one sent to the Project ever comes back. He then finds her severed finger in the hog pen and confronts Cole. Cole says she died of laced speed and was buried on the western acreage. Mandy tells Keno that Tommy was expelled after being caught by the barn, and that she heard he had a camera, which is only hearsay. Reported
The farm fronts an illegal operation run by Cole and Woodrow, with a former missile silo under the barn as a lab. A flashback shows Woodrow offering to finance Cole four years earlier for access to “a resource”, which The Review Geek guesses means his followers. Recaps say Rawlings cares only about profit. We infer that money, and fear of exposure, is why Tommy had to die. No source gives Cole’s reason in words. Interpretation
How it ends
The episode 6 synopsis says the case is about Tommy’s murder, “but countless others as well”. In episode 7, recaps say, Rawlings kills Woodrow and keeps Cole as his partner. The finale synopsis calls it a stand to bring Tommy’s killers to justice. Reported
In the finale Rawlings sends armed men to destroy Echo Canyon. Neagley’s team rescues the survivors and Keno, and Cole is left behind and apparently killed in the blast. Confirmed
Recaps say Neagley then tells Tommy’s parents she got everyone responsible, and Mr. Crane says she is her father’s daughter. Reported
For the full finale, see our ending explained. We found no source that says who the two men in the truck were.
Frequently asked questions
Who killed Tommy Crane in Neagley?
Recaps and Wikipedia say Lawrence Cole ordered it: the hired killer Davos says so in episode 3, and in the finale Neagley tells Cole he killed Tommy. Pierce Woodrow and Arvid Rawlings ran the Tranqlara operation Tommy threatened. None of the transcripts or recaps we read shows who gave Tommy the drug.
How exactly did Tommy Crane die?
At 2 a.m. a man strips and walks toward an oncoming train in Chicago and is hit, according to TV Insider. Primetimer says the drug's hallucinations led him there, and NME says he was killed through the drug.
Was Tommy Crane's death suicide, an accident or murder?
Police were ready to label it an apparent accident, and most coverage describes it as an apparent drug-related suicide. The series establishes that it was murder.
What clues did Tommy Crane leave Neagley?
A letter naming Lake Laverne Summer Camp, a place he hated, and an envelope of rye flour, which episode 2 dialogue says was postmarked the day before he died. A recap says Neagley notes that no journal was among his belongings.
Why was Tommy Crane killed?
He found out what was going on at Echo Canyon and was killed to stop him exposing it. The farm was a front for the Tranqlara trials. A scene in episode 2 has the line "he asks too many questions" and Cole answering "not for long", which recaps read as being about Tommy.
The Tranqlara Welcome Series / 5 emails
Join the Tranqlara Welcome Series
Five short emails over two weeks: what Tranqlara is, Echo Canyon, who killed Tommy Crane and what season 2 leaves open. The first two have no plot details; the last three are labelled [Spoilers].