Beggar's Nest Main Gate
Talk to Gate Captain Ergus. A militia member named Walters has gone missing, and he wants you to find him. Accept the quest, and then fight your way through the undead hordes to The Shining Serpent.
The Shining Serpent
Find Harben Ashensmith and he'll provide you with some background information about the undead infestation. He'll give you some leads, including some strange rumors about the Sword Coast Boys, a local gang (or considering their name, boy band), and about a mysterious cult working in the area. Speak to Drake and he'll tell you about some local citizens who may need your help--Jemanie and Krestal.
Temple of Helm
Before you start digging into the undead problem, finish a few of the local secondary quests. First, stop by the Temple of Helm and speak with Bertrand. He'll tell you about his missing brother, Marcus. Sadly, you won't be able to bring him good news. You'll find Marcus' body to the north, just in front of the gates to the Great Graveyard. Return Marcus' journal and penhold staff to Bertrand when you give him the tragic news, otherwise there's a good chance he won't believe, or reward, you.
Thomas Wheelwright Wagon Repair
Before you enter the wagon repair shop, speak with Aldo and Mattily near the broken wagon in the center of Beggar's Nest. You'll want to clear a path through the undead between them and Thomas Wheelwright's shop. Enter the shop and speak with Hector. He'll follow you back to Aldo, and they'll escape to safety. And if you're curious as to why there aren't any wagon parts in a wagon repair shop, it's because the joint is a front for Tomi's friend Belman. Check the bookshelf in the back and you'll find the forged official document needed for Tomi's henchman quest.
Siril's Bakery
Zombies have invaded this bakery, possibly because they misheard someone talking about the delicious brain muffins. Kill them and search Siril's body for the leaven bread recipe. Give this to Boddyknock once he's told you his story to complete his henchman quest.
Arcane Laboratory
In the northwest corner you'll find a locked building marked with a sundial. If you've accepted the Cloaktower Membership quest, you'll have the key for the door. Inside, you'll find the kindling wood in the woodpile.
The Great Graveyard
One thing is certain: The undead are originating from the graveyard to the north. Unfortunately, the gates are locked. But there is a way in. In fact, there are two ways in. One will take you through the warehouse, following the Sword Coast Boys quest. The other will take you through the Snake Cult Estate, searching for Jemanie's lost brother. Both will lead you directly to the undead base of operations.