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There is more information available on this subject at Flagship on the English Wikipedia.
The UNSC Infinity, experimental flagship of the UNSC Navy.

A flagship is a warship used by the commanding officer of a fleet or battle group. It can be any warship and is not restricted to any particular classification; however, it is typically one of the largest ship types within the fleet, such as a cruiser or a carrier, even an orbital platform. The purpose of a flagship is often for command and control.

Flagships in the UNSC tends to be cruisers or carriers.[1] Although, in smaller fleets, a frigate or destroyer may be the flagship. In the post-war period the UNSC's overall flagship is considered to be the UNSC Infinity, an Infinity-class supercarrier and humanity's largest and most powerful ship.

In the Covenant fleet, flagships tend to be CCS-class battlecruisers or CAS-class assault carriers in the typical fleet. However, in battle groups, the flagship may be a cruiser or, rarely, a destroyer.[2] In particularly large and important fleets, the flagship may even be a CSO-class supercarrier.[3] In a couple of smaller flotillas the flagships were Intrusion-class corvettes. In one case, the flotilla, made up entirely of corvettes, belonged to the Silent Shadow and was used for their operations. In the second instance, the flotilla, again made up of corvettes aside from a single Covenant frigate, was a rogue faction.[4][5]

In the Covenant remnants, the flagships, at least in the smaller groups, tend to be cruisers or in the case of the Kig-Yar pirate queen and Vata 'Gajat's mercenary group, SDV-class heavy corvettes. Only the larger groups such as the Banished, Jul 'Mdama's Covenant and Sali 'Nyon's Covenant have assault carriers as their flagships.

Known flagships

Covenant

 
Seeker of Truth leading its fleet at Alpha Halo.

UNSC

Forerunner

Covenant remnants

Sources

  1. ^ Halo Encyclopedia, page 261
  2. ^ Halo Encyclopedia, page 276
  3. ^ Halo: Reach, campaign level, Long Night of Solace
  4. ^ Halo: Silent Storm
  5. ^ Halo: Oblivion