By default the Flag Commander (FC) is the alliance leader, but the leader can give this responsibility to a player of his choice.
The flag commander protects the alliance flag at his base.
The FC can have 50% extra manpower, to build ships, that can only be used in his 3rd fleet, which is called the "alliancefleet". The alliancefleet can only be used to defend his planet or the planets of his allies.
For information about flag capturing/defending, see Capture the flag.
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