Part of the story is for me defining NPCs and including twists - NPC A might seem like a potential ally, but has a secret agenda. Hints lead to NPC B being a potential enemy, but that's just a false lead by NPC C. And stuff like that. That's story for me. And if I don't have enough time, these things seem often to simplistic. "NPC A is the bad guy". NPC B needs your help. NPC C helps NPC A" with no twists except maybe those that the PCs introduce (like deciding they want to aid NPC A - which rarely, if ever happens. If I add a few twists and ambiguities, either can happen)
Improvising such twists is second nature for me. It helps of course that I rarely present anyone as "good" and "bad", but shades of grey. Then it's just a matter of juggling and twisting stock motivations, and dressing them up in interesting ways.