The Dragon Aerie can be accessed after defeating the boss of Aldia's Keep. After exiting the lift behind the boss room and entering the aerie proper, there will be a short path (ignore the bridge down the sloped path to the left for now) that leads to the emerald herald standing on a cliff to the right. Talk to her to receive an Aged Feather as well as finding out some more story related information. She also mentions that the dragon will welcome you. This is true, it is a friendly NPC unless attacked. Once she is done talking, head back to the bridge we passed up and cross it to reach the first bonfire of the area. Head through the other door in the small room and to the top of the rising path onto a new bridge. An exploding mummy (who inflicts equipment damage upon exploding as well as regular damage) will run towards you from the other side if you get too close. Pick it off with ranged attacks or bait and dodge it's explosion before delivering a counter attack.
Enter the cave the mummy was guarding. At the back, you can find a row of dragon eggs with a blue crystal lizard and a corpse behind them. Kill and loot the lizard and pick up the Radiant Life Gem off the corpse. At the far back of the cave is a slope leading up to an open area guarded by a red dragon. Ranged attacks are your best friend here, The dragon is tough and his melee attacks can take chunks out of your health. His fire breath can be avoided by retreating back down the slope. Melee characters will have to get in close and circle the dragon while baiting attacks. To the right as you enter the open area is another crystal lizard to kill. Several corpses in the area contain: Soul of a Brave Warrior, Boltstone, Dragon Tooth, Darknight Stone. A path leading up to the right leads to another crystal lizard. The hole in this area drops back down into the cave. The ramp next to the bridge has nothing at the top. Cross the bridge here to pick up the Old Radiant Life Gem from the body dangling on the cliff edge. An exploding mummy will be just ahead on the path, so take care of him. Head across the bridge behind where he was standing.
On the other side, a sloping path leads to another exploding mummy and a new bridge (kill mummy, cross bridge... yada yada). At the top of the path beyond is a large white bone gate. If you want to engage the dragon in melee, head on through (but pick up the Petrified Dragon Bone on the corpse hidden behind the eggs on the ranged path first) . For those using ranged attacks you will want to head right at the white bone gate and follow the trail to a slope that overlooks the open area and dragon therein. Smash the eggs at the base of the slope path to find a corpse holding a Petrified Dragon Bone. Ascend the small sloped path nearby to see the dragon below. The same tactics apply here, so go to work. Once the dragon is dead, pick up the items from the nearby corpses: Large Soul of a Brave Warrior and Soul of a Great Hero. A crystal lizard can also be found in this open area.
A tunnel entrance in this area leads to a ledge overlooking the third and final immediately hostile dragon of the area. Ranged characters will want to stay on the ledge, melee will want to drop down and engage him directly. Once the dragon is gone, drop down to the platform below to see a crystal lizard on a platform next to you. You can let it drop down and kill it on the ground. Pick up the items from the corpses here: Soul of a Great Hero, Firedrake Stone, Ring of the Evil Eye +1 and Dragon Charm. Another crystal lizard will be on the other side of this open area. A path blocked by dragon eggs, can be broken through. A lower ledge to the right is a one way drop (meaning a homeward bone exit is required), past the eggs contains two corpses that hold a Pharro's Lockstone and the Large Soul of a Brave Warrior. Either ignore this ledge and head back to the open area we just came from or work your way back from the bonfire. Back in the open area, look for a bridge that crosses over to a zip-line to the left (leading back to the bonfire) and a bridge to the right leading to the Dragon Shrine area. There are a couple of items you can get (Twinkling Titanite and Soul of a Great Hero) by using the zip-lines here (dropping down from one and next to the end of another). Take the time to pick them up if you want and then return to the bridge to the shrine. A wyverrn will smash into the bridge if you delay for too long (the speed is based on how many eggs you destroyed in the area). To avoid it, simply sprint across as fast as you can and step off the other side to reach the Dragon Shrine.