So here's my blind stab in the dark at hacking a story map into Marvel Heroic. It's utterly untested and I'm not quite sure it's even playable, but I thought I'd give it a shot. It was originally inspired by a desire to hack MHR to play Archie Universe Sonic the Hedgehog which has two monthly books, the main book and Sonic Universe, which focuses on the parts of the universe that the main book can't cover.
There are four pieces to the story map. Items are people, places and things and they all have at least one distinction that defines them; groups are loose affiliations of items; relationships are the one way distinctions that connect items or groups; and all of these have a Narrative Stress track.
Milestones give two rewards now: the XP is untouched but the milestones also give either one, two, or three Story Points. A Story Point has one use; to step up the Narrative Stress of an item, relationship or group on the story map.
When a Narrative Stress track is stepped up you narrate just how that item/relationship/grouping is changing. Each step up is an escalation of the situation. When the item or relationship is stressed out the narration of that background story should conclude and any relationships and other distinctions should be redefined to reflect the new status. When a grouping is stressed out every distinction/relationship inside it is changed. Some of the items inside it may leave, others may come in, and so on.
At the end of any event you should have a ton of material to build the next event around if you bring in a few of the items that your players focused on.
I'm not quite sure how this map will be generated. Perhaps with a Pathways session like in Smallville. I'll get back to you all on that.