A fleet's size is limited by the Command Rating of its flagship. Every unit has a Command Rating, as well as a Command Cost. For every ship in a fleet (except the flagship) subtract its Command Cost from the flagship's Command Rating. When the flagship's Command Rating reaches zero (it may not go below zero), no more ships may be added to the fleet.
| Class | Command Cost |
| SB, YDK | Always the flagship |
| BB, DN, SHC | 15 |
| BCH | 14 |
| CC, CCH, BATS | 12 |
| CA. NCA, CWH, CF, MON | 10 |
| CW, CWL | 9 |
| CL, CLC, BS, YBS | 8 |
| DW, DWL, HDW, MB, F-OL | 7 |
| DD, DDL, F-L | 6 |
| FF, FFL, FH, FLG | 5 |
| POL, F-S | 4 |
| Courier | 3 |
| Standard 100-pt minefield | 2 |
| PF/Interceptor | 1 |
| Fighter | 1/2 |
Variants cost the same as the ship they were based on unless the GM states otherwise. A W- or Y-era ships costs the same as its MY counterpart (ie. a WCA, YCA, and CA all cost the same).
"Courier" includes Free Traders (and variants), Priority Transports, and similar ships. FedEx (FX) couriers may only be built and operated by the Federation Express company, and therefore have no CR or Cost.
If, during a battle, a fleet's flagship is destroyed or loses all of its control spaces, fleet command is disrupted for 16 impulses ( turn) while the flag is transferred to another ship. Ships in the fleet may only fire at enemy vessels within 8 hexes; 5 hexes for enemy fighters, PFs, and shuttles. No weapons may be overloaded, but previously overloaded weapons may be fired. Once the flag has been transferred, command is restored and ships which fit in the new flagship's Command Rating are released from this restriction. Vessels which don't fit in are not released until they fit. Active squadrons must be included in the new Command Rating, or they lose their squadron benefits. Once a vessel is included, it may not be released until it is destroyed, crippled, disengaged, or the flagship is destroyed.
Ships may also be organized into squadrons. A squadron consists of exactly three ships of the same class, with one of them designated as the command ship. If the squadron is part of a fleet and the command ship is within six hexes of the other two, the squadron is not affected if the fleet's flagship is destroyed. Squadrons must be designated before the scenario begins. If one non-command member of the squadron is destroyed, the others may maintain the squadron until the end of the scenario. If the squadron command ship is destroyed, the squadron is broken.
If Leaders are present in a fleet, they cost triple the listed amount and up to two non-Leader ships of the same class or a lower Command Cost are free. The ships involved form a squadron. This shows the increased command capabilities of Leader variants, as they can form a squadron with ships not of their class. If a Leader is the flagship of a fleet, it loses all of these effects (but has no Command Cost) and acts as any normal flagship. Command Cruisers have the squadron-forming benefits of Leaders, but don't modify any Command Costs.
Base assault fleets gain +15 to their Command Rating while involved in an assault against a permanent base. In addition, if the flagship is destroyed, the ships may continue to fire up to half of their weapons (count for each type of weapon on each ship; round down) at the base.