Hypothesis: Barry Cain, still secretly working for the NSA, had contacted Lyle Michaels under an alias with a putative tip on Shel. The tip, however, had been a test of Shel: would he talk? When the meetings with the writer continued, Cain decided to eliminate Shel.
Or hypothesis: Barry Cain, like Shel, had been burned by the agency. In the years following their departures, the agency had come to view both Cain and Shel as potentially threatening. The appearance of a liaison between them and Lyle Michaels had been flagged. Shel was killed first because Cain’s position at STX made him too high profile a target.
Or hypothesis: Shel had never left the NSA. When some unknown person within the agency had discovered Shel’s communications with Lyle Michaels, his death became procedure. A whistleblower could make noise too quietly.