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(covers information from several alternate timelines)
In the alternate reality, the weapons bay on Constitution-class starships was located on both sides of the secondary hull along the longitudinal axis, containing numerous torpedo launchers. Situated near the engineering section, the weapons bay contained robotic arms for moving torpedoes from storage, into their respective launchers.
In 2259, the weapons bay of the USS Enterprise housed advanced long-range torpedoes which were loaded into their tubes on the orders of acting captain Lieutenant Hikaru Sulu in an attempt at capturing rogue Starfleet officer John Harrison. (Star Trek Into Darkness)