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Same problem here. Cleared it once yesterday but didn’t have enough bits to a buy an upgrade. Today I got the bits but can’t upgrade unless I clear the bunker; but the door won’t open.
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When you clear the Bunker for the first time you are given one FREE upgrade which is the Valkyrie upgrade on the Rank 1 row. To claim the upgrade simply interact with Rasputin at the Bunker and inspect the Bunker Upgrades icon (brown rectangle top right of his menu). The 4th icon from the left on the top row (Rank 1) should be outlined as available to claim. All you have to do is actually claim it to progress the quest.
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Well, I didn't do that. How do you open the door again?
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Thanks for the tip on the Valkyrie. Problem was that it's barely any brighter than the other icons.