You may have heard that Konquest Mode is a game all on its own, and this is absolutely true. You start out in a dojo with Shujinko as a young boy, and all the other kids in the village are acting out a play. The characters that the children are pretending to be are famous MK warriors, such as Kung Lao, Goro, and Shang Tsung, acting out famous events in the Mortal Kombat universe.
The main missions as well as the side missions there are to do are simply incredible. There is a sick boy who you help by finding medicine for him, or a guard that is hungry and you go to the butcher to get some food for him. By helping people, you can get various rewards such as Kurrency (koins), or being granted access to areas that were blocked off before. Many things such as secret fighting styles will be unlocked through Konquest Mode, so it is important to help as many people as possible.
It's been said multiple times that every MK character will be in this game. The Midway guys confirmed this again at the pre-E3 MK party and E3 itself. Even in this beta version, we are shown characters from Lin Kuei clan members to a messenger for the Elder Gods.
It is this messenger of the Gods that grants Shujinko the ability to develop the fighting styles of all the warriors he encounters. Herein lies in the customization: with all the fighting styles in the game available at your finger tips (through Shujinko), it is up to you to decide which ones you want to use. And you will have every fighting style in the game to choose from; as Shujinko's adventures lead him through the 6 different worlds that Bo Rai Cho sends him to: Earthrealm, Outworld, Netherealm, Orderrealm, Chaos Realm,and Edenia.
One of Ed Boon's answers in MK Online's 10-Question Fan Interview revealed that you can play as Shujinko in Konquest mode until he is an old man, at that point he will be playable in regular Kombat mode as well as online.
In short, Deception's Konquest mode is everything a die-hard Mortal Kombat fan could ever ask for! Check out these videos: