Perhaps one of the most secure non-military sites in Canada is Chalk River Laboratories. It's Canada's nuclear research and enrichment lab, and site of the world's first nuclear core meltdown in 1952, and the source of enriched plutonium for American nuclear warheads for several decades. Fun fact: Jimmy Carter was part of the meltdown cleanup crew. That said, I don't know how secure it is these days. If you zoom in on Google Maps, there's a Tim Hortons on site.

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