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The First Counterattack
You get ahold of this quest by talking to Maverlies in the main courtyard. She'll warn you about the tunnels and inform you that the servants can did up the blockages at any time. We might as well take care of this one now.
Go on down and examine the first group of dead darkspawn. Talk to the mabari. I believe you can calm it with enough Survival. Even if you fail, you'll get a note about a woman named Adria who's hiding in the cellar. This is technically it's own Dragon Age side quest, called Adria's Plight, but we have to take care of it to finish this one.
Advance into the next room and kill the darkspawn here. There are four hurlocks and one emissary. Just rush the emissary and let Oghren grind through the rest. You'll probably get put into Crushing Prison once, but your warriors should just be able to ride it out for a moment. Check the wine cellar for a letter and some loot. Check the prisoner records area for more loot and codex entries. Watch out though, since three shrieks will attack. Cut down the alpha shriek and keep them off Anders.
Look at the books and loot the area. Move forward and get into the dungeon. It's full of ghouls. Just use cone of cold and you'll freeze most of the mob. They're actually pretty weak as long as you can distract a few of them. Once the horde is dead, you can loot the bodies and free the two prisoners. This nets a +5 approval from Anders.
Go forward again to the final room. The other one is sealed off by a cave-in for now. Adria is in this last area and it seems that we're a little late. The ghouls aren't tough though. Try to freeze the mob and just have Oghren rip right through ghoul Adria and the rest of the ghouls with her. Make sure you get some Veridium Ore too. Go to the back after looting all the bodies. Inspect the rubble to end this part of the quest. We'll have to wait for Voldrik to clear the path. You can't go back and talk to the Mabari, so just tell Maverlies that you're ready to go.
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Second Trip and the Shrine
After you do one major quest Maverlies will tell you that the next section has been cleared. Go into the Deep Roads. Go ahead and look at the shrine on the right side. Search the darkspawn's body for a golden idol. You can search the rocks for a key. Then check the offering. Giving it a diamond or the golden idol will open a compartment and give you a fairly nice battleaxe, Frenzy. You can also just take the offering. It's fifteen sovereigns. The two steel golems will attack though, so be ready. I believe that you can also use the corrupted idol that you'll find a whole lot later, but I imagine that you don't want to hoof it all the way back for a minor change in fate.
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Go down the other route into the temple. There are a few hurlocks in each doorway. Just take them out as you go. The trapdoor is locked shut, but the lyrium deposit is important. Check it to get some pure lyrium sand for Bombs Away. Look into the next tunnel to find a gem mine. Once you approach it, a bunch of darkspawn will spawn behind you. There's an emissary too, although Anders was just about able to solo him as they just traded Drain Life spells back and forth. Kill the genlocks and finish off the emissary. Leave the tunnel and go into the next area. You can kill a few more darkspawn. We can only take the route to the left. Kill the darkspawn, raise the gate and go inside. Go in and check the plaque. Then move up and enter the next testing ground.
The warrior test puts you against a lot of skeletons. Just stick close and grind them all down really quick. Check the statue for an inscription. Move on ahead to the next area. You'll come to the bone walk up ahead. Just cross it and enter the big room. There's a tough wraith in here.
He's just a tough shade, but he has a ton of health and some good magic. The Dark Theurge also knows Mana Clash, so make sure that your mage doesn't draw his attention. The good news is that he's alone at the start. You should be able to just surround him and keep getting interrupts. After he's lost half of his health he'll summon about ten skeletons. Use some crowd control magic to help one warrior wear them down. If you're having trouble, send the rogue too. Once they're dead you just have to surround the wraith again. Once he's about to die though, he'll rush over to a wall and go inactive. Your only option is to use the "Strange Apparatus" in the center of the room to zap him and break open the wall. Make sure that you check all four of the urns. There is a ton of great loot.
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Fight to the Barrier Door
Go through the opening and walk up to the blockade. You can go through the hole on the left to move forward. Rob the chest and keep moving. You've got a big battle ahead of you. There's an Ogre Commander and a bunch of hurlocks. Two more will spawn behind you. An emissary will also cast spells like Curse of Mortality and Mass Paralysis, which is pretty rough. I managed to keep everyone alive though. Just keep Anders back and make sure he tosses healing spells and Crushing prison around. Focus on the hurlocks and try to kill most of them before he reaches you. He'll dish out some damage once he's close, but that's about it. Just surround him and keep attacking. You should be fine. Take out the archers, if they're still alive.
We're not done yet though. That wraith decided to possess the ogre, so we have to kill him again. He won't use his abilities though, so it's actually a pretty easy fight. You'll probably just have to pause and drink a few potions to have a quick recover. Once he's dead, you'll get a cutscene. Voldrik will fix up the barrier door and seal off the tunnel. The mission is complete. Head on out.