It is really up to you and whether you like to read a lot of the display info and try the interactive exhibits. We spent close to 3 hours there, but could easily have stayed longer.
The spy mission is an hour. Two hours should be enough to see everything unless you try every single interactive station.
We spent about 3 hours including the mission. We were utterly bored sitting through the spy mission (which was glitchy and basically a bunch of videos), but felt rushed getting through the rest of the museum. Go to a local escape room for a better spy mission experience and spend your time at the museum on the exhibits.
You could easily spend more time there if you are voracious about everything there. For most people, 3 hours should be fine.
2 hours will be good, especially if you have younger kids.
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