"Court Martial" and "The Menagerie" were filmed back-to-back, which was convenient because many of the same sets were used. Even so, the starbase managed to have two different commanding officers, Commodores Jose Mendez and (Aaron) Stone. But why?
The simplest explanation is that Mendez replaced Stone following the events of "Court Martial." Perhaps Stone was relieved of command because of the Finney debacle.
OTOH, it's also possible that either Stone or Mendez was merely an interim commander while the other was absent--perhaps commanding a nearby patrol vessel. Stone's dialogue in "Court Martial" suggested that starship command was something he was no longer involved in, but it's not clear if Mendez felt the same way; if we're to believe that the illusion of Mendez behaved like the real Mendez, it's certainly possible he would have had more hands-on duties than running the starbase.
Malachi Throne was needed for the "The Menagerie" because he was supposed to voice The Keeper's lines, but then why not have Mendez commanding the starbase during "Court Martial?"
--Sran
The simplest explanation is that Mendez replaced Stone following the events of "Court Martial." Perhaps Stone was relieved of command because of the Finney debacle.
OTOH, it's also possible that either Stone or Mendez was merely an interim commander while the other was absent--perhaps commanding a nearby patrol vessel. Stone's dialogue in "Court Martial" suggested that starship command was something he was no longer involved in, but it's not clear if Mendez felt the same way; if we're to believe that the illusion of Mendez behaved like the real Mendez, it's certainly possible he would have had more hands-on duties than running the starbase.
Malachi Throne was needed for the "The Menagerie" because he was supposed to voice The Keeper's lines, but then why not have Mendez commanding the starbase during "Court Martial?"
--Sran