Well, the guy who killed them was a necromancer.
Problem solved.
4th Edition introduced this notion, that I intend to use in my game one day, that undead have three elements: body, mind, and animus (the shadow of a soul). An undead, in it's most basic form, is a reanimated body. No mind, no animus. Zombies, skeletons, basic unthinking no spectacular undead. Give an undead a mind and they think for themselves. Give an undead their animus and they have the same powers they had in life as well as undead specific powers. Vampire Lords, Liches, Larva Mages are examples.
I wanted to run a campaign where the heroes died and where returned to "life" as undead with their animus intact. They're still undead but they can use their powers and maintain their current level. Apply the general undead template (negative hurts, positive heals) and you have a group of adventures under the command of a nercomancer who have their wits about them.
Now you can continue the plot with the addition that the party has to find a way to get free of the nercomaner's control and return themselves to life... or not. Maybe they like what they've become. I like to offer players power with no cost in mechanical terms to see what they do. After all, what is a PC's "soul" to a player? This is the chance to find out.