Woo! \o/ Another Cannon Fodder fan <3
But that's just great if you wanted it to be longer! Best possible feedback there! :D But yea, the navigation needs more pointers and maybe a minimap or something.
And yes you're on to it - the signs on top of the doorways are supposed to lead you to the right room, and the green pulsing spotlight above the correct terminals was meant to lead to the exact spot where you can accept the next phase.
The first quiet phase where you should head to the bridge was meant to give time to get familiar with the place and explore around. I guess it's big enough to get people confused. I'd love to add some voicelines to the exploration phase, like "Hmm.. this must be the communications.." and stuff like that.
But the general feedback is that it needs to be more clear, so more clear it shall be. :)