A ferry is set up when a transport is specifically instructed to move along a certain waypath, designated by the ferry icon. A transport with a ferry associated with it will move land-based units from the starting point to the final drop point of the path. At that point, the ferry will return to the starting point by retracing its initial path.
To set up a ferry route, move a transport aircraft to the point where you would like the route to begin, and select the ferry command. While holding shift, click the ground to create a series of waypoints. The last waypoint will be the ferry's drop off point.
Once you have set the first waypoint, a ferry icon should appear on the ground beneath your transport aircraft. It will remain there until the transport is assigned to another task or destroyed. To order units to board the ferry, select them and then right click on this icon as if issuing a move command. Optionally, you may set this icon as the rally point for one or more factories, and new units will automatically be ferried to the end of the route.
You may assign additional transports to the route by ordering them to assist the transport used to create the route. Select the additional transports, and right click the original ferry transport.
The Ferry command as such is simple, but there are four variations of ferrying.
All factions have the same ferrying capabilities, a T1 and a T2 level transport unit, with higher transport capacity at T2. Amongst the factions the firepower of the transporters vary, with a few minor details. Some gunships have transport capability. In Supreme Commander: Forged Alliance, the UEF gains a T3 transport, the Continental, which can carry up to 28 units, and is heavily armed and armored.
Set up a ferry route
This is the "real" ferry command, and this command has two further variants.
Ferry routes start at the transporter's current location. With the transporter selected issue the ferry command (on menu or F on keyboard) and left-click the destination point. A semi-transparent cross is shown on the map close to the transporter. This is the ferry start point. Holding the shift key down shows a line with arrows from the start point to the destination point, also a semi-transparent cross.
Making several shift-left-click destinations for the ferry command defines the route to take. Units are only unloaded at the final destination.
Use ferry route
Select which units should use the the ferry (as many as you like) and right-click (cursor changes to the load cursor) on the ferry route start point. More units can be added to load later. If the units are far from the start point, and the transporter is not busy, it will fly towards them and pick them up. Otherwise units will move and gather round the ferry start icon. (Mouse-over on units waiting to be picked up shows "<faction> beacon" as their current target in the UI info box)
The transporter ferries units either when it is fully loaded, or if no units are waiting at, or moving towards, the start icon. The transporter will wait at the ferry start point when idle.
If the transport used to set up the route is destroyed, or given new commands, the ferry route is destroyed.
Assist a ferry route
A transporter can assist an existing ferry route. Select the transporter and right-click on the ferry start point (cursor changes to assist icon). If the ferry route is destroyed (the first transport is destroyed) the assisting ferries will go idle, where they are located, loaded or not.
Factory using a ferry route
With a factory selected right-click on the ferry start point (cursor changes to load icon). Units queue up for ferrying on equal terms with those assigned manually. If the ferry route is destroyed, the factory's default destination (rally point) takes effect, ie. in front of the factory.
However it is not necessary for the end of the ferry route from the factory to be the end of the units orders nor to have the transport land into the fighting. Orders after the Move to Ferry order are followed upon landing.
Transport - Load & Unload
You individually load and unload units. The same command sequence is used for the special air transport units, such as Czar and Aircraft carriers.
Load
The load can be done three ways:
- Select the transporter, right-click on the unit to load (cursor changes to (un)load icon)
- Select the transporter, issue the Transport command (menu or U on keyboard), left-click on unit to load.
- Select the unit, right-click on the transporter (cursor changes to load icon).
Unload
Select transporter, issue Unload command (menu or U on keyboard), left-click where the unload is to be (cursor shown as unload icon).
After the load command is issued, and before it has completed you can queue up the Unload and a Move (to get the transporter back to a safe place) using the normal shift-to-queue mechanism. Accidentally issuing the unload command before the load has completely finished, will cancel the load command. For all units capable of transport, they have to be stationary during the load/unload process. Issuing other commands will stop the (un)load process.
Transport assist for a factory
Select transporter, right-click on a factory (cursor 
). Optionally, set or reset the factory move point to a far away location.
The transporter loads units at the factory and then transports them to the remote destination. The transporter will stay loading at the factory until full or the factory build list is empty. If the factory is idle the transporter will wait there. If several transporters assist the same factory they act independently, in particular, loss of one transporter will not stop the others carrying on.
Assist a mass move
Sort of a temporary ferry route.
Select several land units and at least one transporter (typically with a drag box or several shift-left-click), issue a transport command. The transporter(s) will pick up land units "going the same way" and drop them off at the destination. Transporters will return to pickup more units if the distance is "large enough". They will stop at destination. The Gunships with transport capability only take a single trip.
Common for all variants
A transporter will follow multiple ferry or move destinations, but only drop units at the last one. It uses the same path for both directions.
Holding the shift key down shows the route, and any intermediate stops. Mouse-over the destination or intermediate stops (cursor changes to hand icon) enables moving the destination or stops, whithout destroying the ferry route or the transporters activity. New placement takes effect immediatly.
The normal shift-to-queue commands mechanism works for all above.