After making your way through the first three ruins sections, Dubois, the Vault scientist holding the laboratory keycard is found in the caves. He wants to get out of there as soon as possible, as the mother of all deathclaws is near. Unfortunately, it's already too late; the Iniate is knocked unconsious while Dubois is ripped apart and eaten by the deathclaw mother. That means the keycard is also in her belly. Kill her to get it. She's practically blind, and won't know where you are unless you're moving fast, attacking her, or close enough to smell. She'll also regenerate in the radioactive pools if she's hurt.
Once she's dead, get the key and return to Ruins Two, where a previously locked door now can be opened.