I’ve been watching the Spectacular Spider-Man cartoon on Netflix recently. One of the cool things about it is that it freely draws on regular canon and Ultimate canon to create a more unified set of origins for everything. Genetic villains tend to come out of Connors’ lab while tech villains are mostly involved with OsCorp. This suggests to me a fairly simple way of making superhero games feel cohesive.
To start with, make a few core plot nodes; one per player ought to be plenty. Specifically, each one ought to speak directly to the origins and agenda of at least one player character. They can be either concrete things like businesses, labs, or shadowy masterminds, or esoteric things like magical confluences, a particular catastrophe, or a tightly focused theme.
When you introduce a new complication to the story, connect it to one of these nodes. This villain was powered by the same thing that happened to this PC. This natural disaster mirrors the other one that a PC failed to prevent. This new NPC has mysterious ties to that PC’s reclusive nemesis. This connection may be obvious (the PCs are at the lab when an accident creates a new threat) or the source of a long term mystery (who is this mercenary villain working for?). Regardless, it is a primary link that informs all of the future interactions with the complication.
However, each time the complication features prominently in a game, create a weaker connection to some other element on the map (a central node or one of the other complications). This week, the PC’s mysterious girlfriend has been kidnapped by the mercenary villain. Is this just to get at the heroes, or is there something else up? Next week, the unstoppable monster created in the lab comes under the control of the shadowy mastermind. What is the mastermind planning?
Once you’ve got several sessions under your belt, add a few deeper plot nodes: new major complications that change the field or conspiracies that are just beginning to show their edges. Tie each of the original core plot nodes to one of these elements, and then start attaching complications to them as they recur.
Ultimately, you’ll have a pretty deep and cohesive plot web with fairly minimal up front effort. New plots and threats you add become interesting by virtue of having a clear relation to other details the players have been dealing with. Recurring plots and threats become deeper each time they make a repeat appearance (allowing you to only focus development on elements that were a big hit with the players, rather than overly building up a threat that falls flat).
And, of course, you don’t just have to use this for supers games.