This is a water realm, with very nice water graphics (on the surface especially). Your goal here is to turn on the purification tower. You get control of Scree to start with, who has just dived into the water.
Rescue the queen
Immediately head for the temple in the centre. To do this, just head towards the centre, dropping off any ledges you find. Climb up inside the structure, and note that the vortex is going the wrong way. If you look around there is a lodestone. Looking up reveals a platform with a wheel. Climb up, and turn the wheel to invert the vortex direction. Jump in the vortex, and this time you will be taken up.
Climb the NW ladder for a lodestone. Then climb the SE ladder and continue up another ladder to meet the queen. Now jump off the top and climb up out of the centre pit. Heading right to the top of the pit ramp (slightly to the right of the channel on the map) gives you another lodestone; this is by a summoning stone. Head back and hop up the steps that you passed previously. Keep heading north through a tunnel and into a large open area. Run down the ramp where there is a lodestone at the bottom, and climb up the long sequence of steps/ramps to get out of the water and take the undine form to Jen.
To rescue the queen, swim north (towards the arch with the flashing lights) and through the arch into the tunnel. Swim through into the dam lagoon and head towards the dam north, marked on the map. There is a summoning stone by a fish head. Pull Scree through and get him to possess the fish head. There is another lodestone at the bottom of the ledge by the summoning stone, walk down the south wall and head west to get it. Open the fish head mouth, and wander inside and turn the wheel to rescue the queen.
Turning on the machine
Follow aino to the entrance to the purifying machine complex, and learn that you have to turn it back on. Your first job is to fire the system up. Whilst you are in the dam area, if you look on the surface a little south of the dam, as marked on the map, is an island. You can climb out here and pick up a tarot card. Swim through the tunnel into the bay caverns and a fight. Head to the southeast area past some spiky plants (best to boost swim and stay away from the tentacles) to the engineer's room. This gives you a map, and if you press the button, you can activate the gate at the southwest corner of the area. Swim back towards and through the newly opened gate, knocking off a few more undine along the way.
To activate the priming station, you need to realign some cogs. Head to the platform on the northeast surface, and tediously change forms and climb over into the next area and back in the water. There is a wheel here; turn it until the first cog is aligned. Return to the previous area and repeat for the southwest platform and wheel. When both cogs are aligned, head back to the entrance and turn the wheel at the bottom. With the power on, you now need to turn on all the substations.
To start, head back to the engineer's room area. No need to enter this time, just press the switch to open the gate by it and let Scree through. To get Scree through, walk through the gate to the northeast of the fish's head that you opened earlier, and drop down. Walk him through the water current on the north of the caverns area. Just before the passage turns to the east, there is a rock which Scree can push to stop the current flow to let Jen through. Another way of doing this is to walk near the rift gate in the next (bay) area and then it becomes active even though you can't reach it.
Now head up to the rift gate and the beach, and you'll find one of the breakable eggs contains a tarot card (near the water at the northeast side). Use the rift gate to return to the temple lagoon, and enter the water and swim to the substation entrance on the northwest side. Open the door, swim in and turn the wheel to activate the substation. There is also an openable hatch, but it's just for fun. Swim back out and then head onto the dam lagoon (back through the arch you have taken twice before). Head towards the next substation in the southeast. The entrance is blocked, but if you climb out onto the beach a little to the north, there is a tunnel that will take you to the substation. Fire that up and then head to the rift gate in the north. There is a summoning stone here, which can be used to pull Scree through.
Use the rift gate to go back to the beach. Dive in, and head to the circular area on the northwest side. Kill the guard, and press the switch to open the door. Swim southwest past the plants and into the tunnels. There is a summoning stone that you can use to get Scree back. Drop or swim down the hole to the locked gate, watch the cutscene and give it a shove to open it. Up the ladder and in the rift gate area here is an energy fountain and a breakable rock with a lodestone. Using Scree, follow the tunnel to the southwest until you come to a water current. Have Scree push the rock in front of the furthest opening to block it off. Jen can get through by being dragged into the central area by the current flowing into the centre tunnel and leaving by the west tunnel where the current is blocked off. Follow the tunnel to the northwest, kill the guard and head through the door to the fish bones. Head up to the substation and talk to the trapped engineer. Sadly you can't mince the engineer, but you can open the door right back by the rift gate by pressing the switch at the top of the tower just in front of the blender. Head back there.
There is a current in this area, so have Scree walk in. There are lodestones scattered around in the eggs, collect those if you like. When done, head to the south end of the area and turn the wheel to open the control room. Collect the missing hatch part and turn the wheel to activate the kenwood chef. When done, head back to the engineer and use the part to complete the hatch. There is another lodestone by the hatch. Pull the lever to open it and release the engineer, then activate the substation. Head back (again) to the rift gate area where you can now open the final closed door.
Head in and follow the passage where you will be trapped by a rock fall. Kill a few undine, open the door to the southwest, kill another one, and head up out of the spike pit. Kill or ignore the crab. There is a gem in an egg just by it on the beach. Head south and dive into the pool. Climb out to the west. Follow the passage north (with another crab) and head down the steps to a summoning stone to retrieve Scree. Swim down the passage to the north if you want to go back to the rift gate. Otherwise, head up the steps next to the summoning stone, using Jen in ferai form.
For Scree there is a shortcut on the opposite side of the pool. At the top, pull the lever to open the door and head southeast past a couple of crabs. At the bottom is a fish head for Scree to possess. There is a lodestone in an egg too. Climb down to the head, yet another is next to it. Possess the head and open the mouth to fill the pool.
Dive into the pool. Head out and past another crab and back in. Kill the nasties here. Turn on the final substation, and head north past some more baddies to the rift gate. Grab Scree. There is a gem in one of the eggs here. Head back into the water and open the gate at the northwest. Head up into the purification tower and the final battle. Here, you have to fight the king who keeps coming back to life if you bother to fight him. To kill him, help Scree to turn all the wheels. The easiest way is to distract the king by boost swimming around in circles a bit, then when the vents are open, finish him off.
Swim up and climb out, then climb a few ladders. Pull Scree out of the summoning stone to walk up a wall that looks like a metal trellis. Keep climbing ladders until Scree gets to the top, then use the key to turn the whole machine on. Realm complete, back to the Nexus for more cutscenes.