The House of Secrets is completely unrelated to the undead quest. Your task is to reach Source Square where the plague is originating. The rest of the tasks in the Crows Nest are essentially optional quests. If you open every door and hatch you'll find what you're looking for.

If you need a hint...
There is a hatch to the forgotten crypt. It is straight up and to the right if you're entering the crows nest from the shrine (teleporter). Enter the crypt pass a small trial and face a boss somewhere on the other side. That's about as specific as I can get without ruining everything.