Mega Tower

The Mega Tower is located in the mountains north of Nightshade. After beating Nightshade Gym you can enter the cave called Nightshade Tunnel that leads to the Tower.

Tower
Pokémon do not appear in Mega Tower.

You will have to fight every trainer in Mega Tower, no exceptions. Each will have one Lv 55 Mega evolved Pokémon, while yours will be normal. The only time you will have a Mega to use in Mega Tower is when you face your rival after choosing one Mega Stone. Don't worry, you can still get many more Mega Stones!

Mega Lights
The mega lights mentioned above are where you can get more Mega Stones. The Mega Lights show up as white glowing discs all around Godra after you've beaten the Mega Tower. Walk up to the lights and click on them to get a Mega Stone. The lights have fixed locations in the game. Here is a list of where you can find all the Mega stones:
 * CHARIZARDITEY in map 002: Cloudvale
 * HERACRONITE in map 134: Route 3
 * GYARADOSITE in map 139: Abyss
 * GARDEVOIRITE in map 157: Route 5
 * GENGARITE in map 157: Route 5
 * BLAZIKENITE in map 158: Route 5
 * GARCHOMPITE in map 158: Route 5
 * BANETTITE in map 159: Route 5
 * BLASTOISINITE in map 160: Route 5
 * AMPHAROSITE in map 166: Route 4
 * ALAKAZITE in map 168: Shadowfell
 * KANGASKHANITE in map 174: Route 8
 * LUCARIONITE in map 176: Vespore Lake
 * VENUSAURITE in map 178: Orchid Town
 * AGGRONITE in map 179: Route 6
 * ABSOLITE in map 190: Route 7
 * MANECTITE in map 191: Route 7
 * ABOMASITE in map 192: Alder Town
 * MAWILITE in map 197: Route 10
 * MEDICHAMITE in map 203: Route 12
 * MEWTWONITEX in map 206: Route 13
 * MEWTWONITEY in map 207: Route 13
 * AERODACTYLITE in map 225: Feverfew Desert
 * HOUNDOOMINITE in map 244: Rantipole Island
 * SCIZORITE in map 257: Feverfew Desert
 * PINSIRITE in map 266: Feverfew Cave
 * TYRANITARITE in map 279: Ebony City
 * CHARIZARDITEX in map 306: Mega Tower
 * MEWTWONITEX in map 407: Biyu Island
 * MEWTWONITEY in map 407: Biyu Island

Mega Stones
They work! I've seen it firsthand with Gengarite. Although the Mega Evolutions are a little wonky visually... they definitely work. My Gengar's stats seem to change when Mega Evolved, although I cannot be sure if it actually does change.Two Mega Evolutions CANNOT occur in the same battle. (I tried it with my Charizard and Gengar)

Challenge Cave
Next to the Mega Tower there is an old man guarding a cave entrance. When you talk to him he says that you are "not yet ready" to enter.

In actuality, this cave has not yet been implemented in the game (as of full game version 1.0). The old man only has one line of dialogye (the "you are not ready" one), and the door behind him has no event attached to it.