This are two ideas that I've always loved to see since the original ISS. I think that this game would definitely benefit from a special "Story" mode, along with a more dedicated Co-Op that players could participate in which would be a PvE gamemode and could be progressed forward with community writing and involvement/design. Players would have a set of objectives to complete (which could be a re-use of the existing mission system code that was present within ISS). Similar to Battle Royale, players could receive rewards and have leaderboards stats for this mode like "Objectives Completed", "Players Revived", "Matches Played", etc. and maybe even work on implementing special boxes/items that could be built around player interaction and working together to win.
Story Mode: Players queue up with a party of various amounts of people (Maybe 5 max?) to go along with a storyline. The camera control system used for the bus could be re-purposed to include cutscenes and function the story along. Players could be put on various maps and timelines (For example: A campaign where players are the Military and have to work towards covering up the outbreak. This would involve Burning bodies, executing groups of survivors with inside information, destroying radio towers, etc.) Safezones could be used for players to catch a breather, similar to checkpoints and other things like Safezones in a Left 4 Dead Campaign. Various Storylines could be added, and even connect together to continue the game's timeline. This could work well in a early-apocalypse timeline as a lot of buildings lack overgrowth and don't have as much "broken-down" design. This could also allow more people to assist with development by writing stories and suggestions for campaigns/objectives as well as inspire players to try the gamemode out regardless of whether they win or lose. Players could earn rewards based on progress as well, with the ultimate reward being for completing the campaign.
Players are given a location to barricade and cover up in with a starting loadout of items similar to the Battle Royale system, which is a wave-based system. Players face off against zombies in a co-op mode, with boss waves every 5 and 10 increments. Wave 5 would be a Super Zombie, with 10 Being an Alien Super, and increasing in number of zombies/super-zombies/aliens depending on the wave players reach. This could come with a "vending machine" system where players can purchase items based on what is needed (Weapons, Ammo, Shields, Etc.) and could get access to better items as more waves go on, with leaderboards being available based on waves finished, zombies killed, players saved, supers defeated, etc. and could even come with it's own steam achievements or special boxes/items similar to Story Mode Rewards.
How would Reviving Players work?
When a Player dies, they have a 15-20 second "down" state in which players could use a syringe or other item to resurrect players and bring them back, but each player could only be revived once or twice to add to the tension. Loot drop would be disabled to keep tension even higher, to discourage players from just looting their dead comrades and trying to strong-man the whole mission. There are some other suggestions and ideas I can formulate about how all this could work, as well as any other questions that I'd need to define. Thanks for taking the time to read the post and I hope that you'll take my suggestion into account.