In February 1962, Thornley completed The Idle Warriors, which has the historical distinction of being the only book written about Lee Harvey Oswald before Kennedy's assassination in 1963. Due to the serendipitous nature of Thornley's choice of literary subject matter, he was called to testify before the Warren Commission in Washington, D.C. on May 18, 1964.The Commission subpoenaed a copy of the manuscript and stored it in the National Archives, and the book remained unpublished until 1991. In 1965, Thornley published another book titled Oswald, generally defending the "Oswald-as-lone-assassin" conclusion of the Warren Commission.

In January 1968, New Orleans district attorney Jim Garrison, certain there had been a New Orleans-based conspiracy to assassinate John F. Kennedy, subpoenaed Thornley to appear before a grand jury, questioning him about his relationship with Oswald and his knowledge of other figures Garrison believed to be connected to the assassination. Thornley sought a cancellation of this subpoena on which he had to appear before the Circuit Court. Garrison charged Thornley with perjury after Thornley denied that he had been in contact with Oswald in any manner since 1959. The perjury charge was eventually dropped by Garrison's successor Harry Connick Sr