Not sure, if this is similar issue, but I am also stuck on this quest, while the quest is pointing to a specific gate, I cannot operate the gate, Tommy's around are not helpful. I can only assume, I should somehow either enlist to Tommy's or do some quests for them, but I have met many Tommy checkpoints, spoke to every single Tommy I found, no one offered me to join or start a quest. Ironically, only one opens a dialogue, near the gate that Heavenslayer quest mark is pointint to, but he just declines my entry, saying my name is not on the list "You are not important, I am not important, only this list is important and your name ain't on it."
So I am traveling aimlessly, hoping to trigger the Tommy quest (that also should get me a functioning gas mask, as the last places I did not visit are full of tunnel cough... of course also the places behind the closed doors, which I cannot pass, as well)
But if your game is not even giving you quest-marks on the map, that sounds even worse.