It was taken out due to IG events with the flooding of the sewers, but it was one of my favorite quests. I love the defend against the waves kind of quests.
Maybe move it into a portion the Machine.
That would be great! Perhaps moving it to the Bowels or Maintenance Shaft?
Agreed, but change it so that it's a Covenant quest.
I think the less faction specific you can make it, the better.
Well it was always faction specific you got hired by an Auxiliary to aid an agent.
So in this instance maybe it'd be hired by someone from the Fortress in Lower to aid a Primal Cave Cultist or what have you.
The Covenant do something to flood the machine without DM supervision, maybe have an ability for Engineers & Warders to pump the water back out of the Machine & Sewers without supervision.
When the water level is raised too much, the quests in those areas can't be done anymore (and maybe Covenant gets a small XP bonus once a reset for visiting these areas in this state), and when the water level is lowered enough, re-enable those quests back.
There were more quests than that one defence quest that got jilted out of accessibility (books, chosen) that were fun to do
Moving the defence quest to the maintenance shaft instead seems the most plausible location to retake it though as per Kinslayers suggestion.