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I have a question in terms of deployment of troops kept in reserve.

Per deep strike rules, you say what is staying in deep strike reserve vs normal reserve.

However, if you keep a unit and a transport in reserve, can you decide after deployment to bring them on separately or do they have to be declared as being embarked and in reserved during deployment?

For example:

Necron Deathmarks can deep strike and take a Night Scythe as a transport. If I don't declare them as deep striking, do I have to say they are embarked in the Night Scythe or can I choose to bring them on embarked or not later?

You do not have to Prepare the unit in the Transport; But If you do you must come in with it, and If you prepare them separately you cannot have them come in in the vehicle.

IE they come out of reserves exactly like they went into reserves.

 Unholyllama wrote:
Necron Deathmarks can deep strike and take a Night Scythe as a transport. If I don't declare them as deep striking, do I have to say they are embarked in the Night Scythe or can I choose to bring them on embarked or not later?

You can have the Night Scythe fly on and the Deathmarks Deep Strike.
You can have the Night Scythe fly on and the Deathmarks walk on.
You can have the Night Scythe fly on with the Deathmarks embarked.
You can have the Nighr Scythe fly on with the Deathmarks deployed with the rest of your units.

And the decision amongst those 4 options must be made during deployment, not when your reserve roll succeeds.