I played this game when I was real young. We had the demo.

The mission was fighting a gigantic ship which had other ships attached to it.

The idea was to take out the incoming ships until the mothership was weak enough to attack (or at least that's how I played it)

there was a convoy to protect, which was impossible for me to do and also, I believe, optional.

Anyone know which mission this was? Anyone have any footage? I've found a lot of old games I used to play but this one eluded me, and I'm still waiting for the 'eureka!' moment.

As far as I remember there where more than one of those missions like the one you describe in the original I-War game, one that included a biobomber, one with transportships launching fighters and one with a huge conveyor type transport flying in LDS space.
I couldn't find any complete I-War playthrough on the tube, maybe you are more succesful.