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For comics, the mid-80s saw the birth and proliferation of the "crossover event". For good or ill, these were generally memorable and required characters to show up across the entire line (often with slim justification for series that didn't take place in the contemporary DC setting). Now, you're running a game in a shared comic book universe (DC or Marvel work equally well), which is the equivalent of a comic book series. Shouldn't those heroes also heed the call about once a year/dozen sessions? Our last game lasted long enough for us to take part in two crossovers - Millennium and Invasion. Here's how I did it...
In Millennium, the Manhunter robots got close to someone in every series and tried to either kill them, turn them or undermine them somehow. Some Manhunters were disguised as supporting characters, others brainwashed close confidants like Lana Lang. Since I ran one of the heroes as a base-bound NPC, I had the players interrupt his kidnapping. As a series that took place in 1987 (in this case), they just HAD to have a Manhunter in their midst. But I didn't stop there. They had to show up in the main crossover series. That's easily done: Flip through the mother-series and find all the big group shots.
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Don't be afraid to let your heroes change history! That's one of the reasons using old crossovers works well. You already know the outcome and impact (or lack thereof) of any given event, so it's easier to let changes be made, or know what to keep intact. 20 years on (as it was), I knew Booster didn't need this win to keep going. When we did Invasion, I of course had the players fight Thanagarians or whatnot, but I also allowed them to succumb to the gene bomb if they wanted to change their powers dramatically. The most memorable group shot for them was the big superhero hospital.
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Yes, you could try to do crossover events in real time. Fight zombie Black Lanterns or Norman Osborn's HAMMER. But when you can't be sure how those stories will end, or what will occur in their wake, you're rolling the dice more than usual. And if you don't wait for them to be over (and let's say they don't come out with untold chapters and aftermath mini-series ad infinitum), you might be left waiting a looooong time. They don't make them as monthly as they use to, do they?
My new game - Time Masters - is primed to take part in just about any crossover published at any time (just like the Booster Gold series), I do well to remember all this. It may not be too long before I point to the insides of a comic and ask "where do you wanna be in this crowd?".
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They're even available for free download on a number of fan sites for the system. (classicmarvelforever.com has all the published modules and rulebooks, though not all of the maps and accessories that went with them).