Instructions
Leave the research center, and travel north through the two empty structures to enter the first puzzle chamber. Walk up to the panel in the center of the room and press "A" to examine it.
Drag the loose tiles into the picture of Kabuto to complete it. Hold your stylus on a tile to rotate it. Once the picture is complete, a hole will open up in the floor, and you will fall through it to the next level. A scientist will give you the Unown Report to keep track of the various Unown forms, and Unown will begin to populate the Ruins.
Head west and follow the path until you reach a ladder. Climb the ladder to return to the first floor, exit the chamber and then walk south.
Surf on the water to continue south, and then walk southeast once you return to land. Walk into the cave to enter the second puzzle chamber, complete the picture of Aerodactyl in the middle of the chamber and then exit the chamber again.
Travel to Route 33, the road leading east out of Azalea Town, and enter the Union Cave. Take the stairs in the northwest corner of the cave down to the lower level, surf north across the water and continue northwest. Climb the northern set of stairs, surf north and then exit the cave to return to the Ruins of Alph.
Follow the path to the south to enter the third puzzle chamber. Complete the picture of Ho-Oh, and then leave the chamber.
Enter Union Cave again and return to the lower level. Surf north, and then head west toward the southern set of stairs. Push the rock out of your way with a Pokemon's Strength move; then exit the cave. Enter the building to the right of the cave, and then complete the picture of Omanyte in the middle of the chamber.