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Brothers of Stone
You can go down the right path at the threeway split in the temple to go to the a darkspawn camp. Just past the camp, you can talk to two statues. There's a statue of war and a statue of peace. War wants you to disturb a magister's grave and kill his spirit. Peace will want to talk to you afterwards though. He wants you to convince his brother to give up his thrist for vengeance.
You can go disturb the bones and kill the magister's spirit. The magister's bones are just a little ways back, close to the magic circle. He's a tough mage but he's all alone and easy to kill. Just surround him and kill him. Go back to war and you can get a decent sword.
If you want to follow Peace's plan, you can talk to War and use persuasion to let him seek peace in his lot in life. This doesn't mean you can't double dip though. The bones are still there and you can still kill the magister
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Ines the Botantist
I believe that you have to talk to Wynne in Amaranthine to get this one. She's standing outside the Chantry and wants you to find her friend. Ines is needed for an important vote on whether the Circle will rebel or not. You can add your own comments if you wish.
Surprisingly Ines really is just a botanist. I was expecting another Blood Mage planning to be immortal. Oh well. She's behind the darkspawn camp on the right side of the forked path. She's far back though and behind The Old One, a very powerful sylvan. Don't just rush in at half health. Once you talk to her, she'll say that she really just wants some nice plants and doesn't care much for Wynne. If you agree to get her some Northern Prickleweed seeds, she'll promise to go to the meeting of the Circle. The seeds are literally right next to the path back to the temple. You will run right past them when you try to leave. Grab some seeds from the plant and give them to her. She'll give you some potions and recipes and then promise to leave now and go to the meeting.
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The Summoning Circle Puzzle
I'll be honest. I got lucky with this one. You need to activate all the stones and have them all connected by fire. Here's the rough way I did it. You start by pushing in the missing stone. If you read the codex, you know that you need to connect all the stones with fire. You move it along like a snake.
Do not go to the outer edge with your first move. Start by moving to the middle circle. Fill it out, but watch the inner pentagon. You want to move into it when there are only two paths back out to the middle circle. Curve in, fill out the pentagon and then leave with the last route out. Finish the middle circle and go to the outer one. You should be able to just run it around to fill out the circle. After this, there should just be one or two stones left to click. Fill in these little "missed" spots to fulfill the puzzle. A magic chest will appear in the center with a necklace called "Illumination." It boosts all attributes by three and mental resistance by ten.
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You can get this one in the SIlverite Mine. Keenan is a wounded soldier just past the second experimental subject. You can talk to him and he'll only ask that you get his wedding ring back from the darkspawn that crushed his legs. He then wants it delivered to his wife. He dies shortly after telling you this.
The guilty darkspawn is the dragon tamer. He's in a side tunnel after you kill the last two experimental subjects. You also want to go here and kill him, because the fresh dragon egg is necessary for crafting a sword from the eldest dragonbone.
Killing the dragon tamer isn't hard. The real challenge is killing the drake he has. Each just needs to be surrounded and beaten to death. Loot the ring off of the tamer's body. Once you've escaped, you can take it to his wife in the Amaranthine inn. She's with her new partner though. It seems that she wasn't too faithful. She'll accept the ring and be saddened by his death though. You can pick your choices here for yourself.