After beating the Elite Four activate the center statue and it will lower you to a new sub floor. Climb the stairs and see that N has beaten Adler. N will then summon his castle and invite you inside so you might as well follow him in. You'll be greated by the Seven Sages (minus Ghetsis) and the gym leaders you fought will come to keep them busy. There are no wild Pokemon here and there are no battles until the end so just explore the rooms on the next three levels and get all the items.
Room 1: Empty
Room 2: Heal with the lady on the left
Room 3: Item
Room 1: PC
Room 2: Item
Room 3: Guy will transport you to the League and back
Room 1: N's. Item
Room 2: Item
Room 3: Nothing
Then down a long hallway and up a long stretch of stairs and you are at N. He'll say how he is disappointed that you haven't gotten Zekron yet and then BOOM. The Dark Stone will activate and it's Pokemon catching time.
Zekrom / N / Ghetsis
All of these battles happen one after the other automatically with full auto healing for your Pokemon party in between.
LVL 50 [Dragon / Electric]
This is a good battle to just go ahead and throw the Master Ball for the auto catch right away at the start. It's important to the story for you to catch it. Ice, Ground, and Dragon type attacks will do massive damage and depending on your level could easily OHKO. Fire, Grass or Electric will do half damage so you can walk your way down. A Cobalion with False Swipe and Thunder Wave for leaving 1 HP and Paralyse will really help you if you want to try to catch the old fashioned way with a Ultra Ball.
N will heal you up afterwards and then it's right into the battle with him.
Reshiram - Lvl 52 [Dragon / Fire] - Weak to: Ground / Rock / Dragon
Carracosta - Lvl 50 [Water / Rock] - Weak to: Grass / Electric / Fighting / Ground
Vanilluxe - Lvl 50 [Ice] - Weak to: Fire / Fighting / Rock / Steel
Klinklang - Lvl 50 [Steel] - Weak to: Fire / Fighting / Ground
Zoroark - Lvl 50 [Dark] - Weak to: Fighting / Bug
Archeops - Lvl 50 [Rock / Flying] - Weak to: Water / Electric / Ice / Rock / Steel
And right after that you are healed and Ghetsis will come at you with everything he has.
Cofagrigus - Lvl 52 [Ghost] - Weak to: Ghost / Dark
Bouffalant - Lvl 52 [Normal] - Weak to: Fighting
Seismitoad - Lvl 52 [Water / Ground] - Weak to: Grass x4
Hydreigon - Lvl 54 [Dark / Dragon] - Weak to: Ice / Fighting / Bug / Dragon
Eelektross - Lvl 52 [Electric] - Weak to: Nothing due to ability
Bisharp - Lvl 52 [Dark / Steel] - Weak to: Fighting x4 / Fire / Ground
N's Castle - Ending Sequence
After that enjoy the end credits since you just won the game for the first time. After the credits load your save and you'll be back in your home with a lot of new stuff to do and a lot of new route to see and Pokemon to catch!