Flagship

A Flagship is a ship that commands operations in a Fleet, not just a classification of ship and can sometimes even be an orbital platform. It can be any warship and is not restricted to any particular classification. This is the ship that houses the Commander of the Fleet/Armada/Battlegroup.

Speculation
It is possible that Battlecruisers and Carriers are usually the Flagships of a Fleet or smaller unit structure.

Covenant

 * Seeker of Truth: Unknown
 * Ascendant Justice: Unknown, likely a Reverence-class Cruiser
 * Sublime Transcendence: Covenant Supercarrier
 * Incorruptible: Reverence-class Cruiser
 * Shadow of Intent: Covenant Assault Carrier
 * Truth and Reconciliation: CCS-class Battlecruiser

UNSC

 * Forward unto Dawn: UNSC Frigate
 * Trafalgar: UNSC Supercarrier
 * Hopeful: Mobile Battlefield Hospital
 * Leviathan: Marathon-class Cruiser
 * Pillar of Autumn: Halcyon-class Cruiser

Related Articles

 * Capital Ship
 * Covenant Fleet
 * Covenant Navy (Service)
 * UNSC Navy