The Morrow Project was supposed to wake up three to five years after the nuclear exchange and the Atlantis Project was slated for 75 years later. Presumably to get support from a reforming North America.
I would place it in North Africa (all low priority targets widely dispersed), Southern Spain, South of France, or an Aegean Island.
The Aegean Island fits the most, mythological Atlantis was an island, and this would be the easiest to conceal construction and other operations prior to WW3.
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