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Because of the Sovereign class’ heritage as a purpose-designed warship, they have facilities for more and larger auxiliary craft than most Starfleet vessels. The Main Shuttlebay on the Independence occupies most of the aft portion of the Primary Hull from Decks 6 to 9 and can support a variety of types including multiple Runabouts and all standard Starfleet shuttlecraft. The Secondary Shuttlebay is located in the stern of the Engineering Hull and, while slightly smaller, can support this wide variety of craft as well. Both bays have dedicated Tractor Beam emitters and atmospheric containment force fields in addition to large segmented doors that are typically closed when the bay is not in use. Both Shuttlebays contain maintenance shops and dedicated parts replication units. Vehicles smaller than Runabouts are typically parked in alcoves to either side of the bay, or in below-deck hangers accessed by elevator platforms.

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