| All righty... [warning: serenity plot spoiler]
In a siege, food and water supplies are paramount. Send the party on a quest to get wagons of water and carts of food into the city. They have to get out without being seen, stealthily search for supplies, find them, and somehow get enough of them back to make a difference. Possible solution: reduce item.
Fetch the plot coupon: Go out, find an army, convince them to be reinforcements. This can be a mercenary company, a neutral noble, or the Serenity solution: tick off a bunch of barbarians and lead enemy B to fight enemy A.
We're all going to die, so here's what YOU'RE gonna do: The PCs' job is to escort the women and children to a safe haven. The commander has NO troops to spare on this task.
In addition, you could just let them be military commanders. Let them fight mobs of soldiers (DMGII). Let them run the defenses of a sector, as if it were a war game. Come up with a quick and dirty system for mass combat, give the players the rules, and let them run things. There's several systems out there for d20 mass combat, you could pick one of those.
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All role playing advice is given without knowledge of you and your group. Only you and your group knows what is fun for you. What you are doing is not badwrongfun. My advice is offered based on what I think might be fun for you to try.
"Art is the demonstration that the ordinary is extraordinary." - Amedee Ozenfant, Foundations of Modern Art
"I already have a place where I can get little recognition for my accomplishments, advance at a very slow pace, and have to work hard to eke out minimum rewards for my efforts. It's called work." - toberane.
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