OK. I'll put it in a nutshell:
The Prologue isn't related to the main Wing Commander plot so i'll simply tell you the things you should know about the story to understand the WC:Saga plot:
Story:
Humanity is in war with the Kilrathi empire (a cat-like and very aggressive species) since more than 30 years. After some important terran victories (thanks to the hero of the original games Colonel Cristopher Blair) the Kilrathi were about to lose the war.
Nevertheless they managed to fool Confed into a false armistic and launch a surprise attack on earth. After destroying a handfull inner terran colonies and hitting some of earth's most important cities, the terran fleet finally manages to beat them back and save earth but the fleet also sustained heavy casualties.
However the Confederation has never really recovered from that blow and after another few months of fighting the Kilrathi are winning major victories against Confed and now you(the heroic fighter pilot) has to do your best to help Confed in realising a daring plan to defeat the Kilrathi.....
Gameplay(compared to FS):
-Just like in Freespace there are intersystem jump nodes. However there are no insystem subspace drives (This is why you cover long distances with the autopilot).
-Capships are a lot of more fragile than in FS. One to three well-placed torpedeos can take down any capital ship. So watch out if you have to protect one.
-Missiles are deadly. Deadly for your enemy and deadly for you.
-You can't modify your gun-loadout.
-You have only a limited amount of afterburner fuel.
-Unlike the blob turrets in FS the turrets in Saga can get you killed.