After defeating team plasma at the relic castle you go to Nacrene City to receive the "Dark Stone" an item described as Zekrom's destroyed body. The stone will remain dormant while you defeat the 8th gym and during the Elite Four. After preparing to battle the Champion you will find that N already has beaten Champion Alder using his own Reshiram. After N commands the ancient Team Plasma castle from under the Pokemon League to emerge. After you enter the Castle the six sages will attack you but all the gym leaders of Unova with the exception of Chilli, Cress and Cilan will defend you and battle the sages. You will then go to the highest floor of the castle. Along the way heal your pokemon. Once at the top you will find N who will command Reshiram to come by his side. After Reshiram appears the Dark Stone in your bag emerges and turns into Zekrom who you will then be able to catch:
Zekrom, Lv50 Dragonbreath Slash Zen Headbutt Fusion Bolt
After capturing Zekrom you will have to fight N who will have a Lv52 Reshiram. Note: Use Fusion Bolt on your first turn and Dragonbreath as your second and so on until Reshiram is defeated. Reshiram will always use Fusion Flare first so you will get a boost for Fusion Bolt as the moves effect.You can awaken Zekrom from the Dark Stone by challenging King N and Reshiram at the Pokemon League, in the final encounter.