1. I activate my MK2 to do some stuff and I spend the dial. Opponent goes after.

2. I now choose to activate my CR90 with Leia on board.

3. I reveal the navigate command.

Does Leia affect the next face down command, or face up (thus being useless)? What qualifies as "top command" - from Lea's card text?

The next face down command; the one face up has already been spent or discarded and is no longer part of the command stack (so it can't be "the top command" that Leia manipulates). It is placed on the ship card , i.e. removed from the rest of the stack, as an indication that the ship cannot be activated again.

RRG p.3, Command Dials :

When a command dial is spent or discarded, it is
placed faceup on the ship’s ship card and remains there
until it is assigned as a new command during the next
Command Phase.

What he said, the face down dial on the top of the stack.

What he said, the face down dial on the top of the stack.

Thanks mates.