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In that year, the captain put in a request prior to stardate 41603 for a refit of the transporter system. She was informed, in three orders, by Admiral Gregory Quinn of Starfleet Operational Support Services that Starfleet Command wouldn't make a decision on the request until the ship returned to spacedock. Later that year, these orders were read by Lieutenant Commander Data during an investigation into an alleged conspiracy in the highest levels of Starfleet Command. (TNG: "Conspiracy" okudagram)
In 2365, Dick Brownfield was the commander of the Atlantis. In that year, the ship was assigned a diplomatic mission to Alderaan. The starship was named on a Starship Deploy Status chart that was on display at the courtroom of Starbase 173. (TNG: "The Measure Of A Man", okudagram)