The short answer is: any order you like!
The long answer: We'd suggest that you start with Season 1 Mission 1 and go through the story chronologically. You can fit in any additional content wherever you like, but here are some general pointers.
- Zombies, Run! 5K Training is set between Season 1 Missions 1 and 2 of the main Zombies, Run! story. The story in this app largely has no impact on the main Zombies, Run! storyline.
- Supply Missions all take place between Mission 1 and Mission 23 of Season 1.
- Race Missions are set around the end of Season 1, but you can play these after you've finished the Season. You can complete a single race mission over multiple runs. You don't need to run these, though, as all the information will be revealed in Season 2.
- Virtual Races all take place before or during Season 1, or otherwise outside canon, and are designed to have few if any spoilers.
- Airdrop Mode and Interval Training take place sometime during Season 2, but standalone. These are only available to Legacy and Zombies, Run! subscribers.
- Season 2's Side Missions are Halloween-themed and are fun, completely standalone extras that do not have any impact on the story at all.
- Radio Mode seasons are specific to their respective Story Mode season, and will contain spoilers if you listen to them ahead of time.
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Home Front missions do not contain spoilers for the main Zombies, Run! storyline, however they do contain characters who show up starting in Season 2 and Season 5.
Note: We've added this timeline because we get asked this question a lot, but you don't have to play the missions in this order at all. If you want to start from the last mission of Season 3 and work your way backwards that is totally okay!
If all your friends are on Season 2 then you can skip Season 1 and come back to it later. You should feel free to play missions in whatever way you like because the game won't punish you for not playing in a specific order.