Just so we are on the same page, Gatekeeper is the robot / mecha boss on the Station Passage, right? There is one dungeon after that, the CEO Office Area, the boss of which is Belphet, and which concludes the story.
I do not really remember exactly, but maybe you have to beat the Gatekeeper twice, like some of the other bosses, to advance to the Office Area. I could have sworn, however, that the Endless Nightmare gets opened only after beating Belphet (it did in my case, but maybe you can find the Access Card on the Subway level, too), so I
am a bit confused there ...