Starbase Command was the organization in control of Federation starbases.

After Spock had taken over the USS Enterprise with forged orders in 2267, he told the bridge crew Starbase Command had assigned Captain Kirk medical leave until the ship's return. (TOS: "The Menagerie, Part I")

When Doctor Beverly Crusher was caught in a shrinking warp bubble in 2367, she imagined that Captain Jean-Luc Picard gave her the advice to contact the Starbase Command of Starbase 133 to find out what was wrong with her universe. (TNG: "Remember Me")

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