The world is ruled by dragons. A guardian dragon for the nether, end, and over world. These created their own worlds in the way they saw fit. The dragon of the over world rules over the people there, protecting them, and keeping away evil, like zombies and giant flesh eating spiders. The people had a vast empire with castles, wizard towers, farms, towns, markets etc. These were the relatives of the testificates.
One day, the elders of the civilization, who were excellent bow hunters were out hunting and were attacked by a group of red dragons, from the nether. This was a terrible omen. The nether and end dragon had teamed up and tried taking over the over world. They fought the dragon guardian of the over world, eventually beating her and imprisoning her deep underground under the tallest mountain in the land, but not before an epic battle that crumbled mountains, left giant water filled craters, and tore huge ravines in the earth.After the fight was over the Nether dragon took half the people and enslaved them, turning them into zombie pig men and taking them to the nether, the ender dragon took the other half to the end and transformed them into endermen.
The dragons then destroyed the people's civilization, wiping it off the map like it was never even there, everything that is ....except for the places under ground.After the complete destruction of their civilization there were still some un-enslaved testificates, including the testificate elders hiding out underground in the mine shafts and strongholds. Knowing their land would be destroyed and all signs of their once great civilization demolished, before hiding they took what they could of their culture to preserve -their music. They hid them in chests where they could -in mine shafts and strongholds.... the only structures that might remain... While recording a disc with instructions on how to beat the nether and ender dragon... last disc.... (disc 11), they were found. The elders tried to escape but could not. The disc was broken but playable.The elders and remaining testificate families were brought to the surface. As punishment the elders were cursed and turned into skeletons and turned evil. They were armed of course with...their bows. The portals to take the enslaved testificates to the nether and end were closed. The only option The ender dragon had was to erase their memories so that they would not remember what had happened and pose no threat to restoring the over world dragon guardian.
The ender dragon ordered the endermen to erase the memories of the remaining people. This is their power, by staring at the people, all their memories of their life before their dragon guardian was imprisoned was erased forever.Of the remaining families there were two brothers who were not affected by the endermen's gaze. After it was done they tried explaining, and pleading for the people for help...but they did not remember. The brothers left their people knowing they were the only hope to save their dragon and bring order back to the monster infested lands.After surviving in the woods for months they learned how to craft tools and build to survive. But the dragons of the netherworld's caught on to their escape and the unique ability they had to be immune to the endermen. They sent out hunters...The younger brother was found by the enderman hunter. He tried fighting the endermen but lost...
The older brother couldn't help...he was too late. Frantic to find a way to save his younger brother he remembers the teachings of an elder about building a portal to 'another world'. it's his only hope. He builds it and travels to the nether, where he finds his brother imprisoned in a nether fortress and frees him. But before making it back to the portal they are stopped by blaze guards. The guards call the older brother a foolish hero.... in netherspeak, "herobrine" For his feeble attempt to rescue is brother. The blaze then begins channeling a spell to banish him into the void -a forsaken place between worlds... Herobrine starts to fade "Help me brother, help me Steve!" Before the spell is completed Steve interrupts it and stabs the blaze in the heart. With Herobrine's voice fading Steve listens carefully.."Restore our world, kill the ender and nether dragon. Free our guardian and bring peace to our world. With our guardian restored it will break the curse on our people, they will come back, they will remember. But to aid their memory you must build something worthy of their return. You must....build the world. You must....save the world."Herobrine pushes Steve into the portal. Where he appears back in his once familiar land now void of anything his civilization has built and accomplished....and the only one who can save it.
The older brother couldn't help...he was too late. Frantic to find a way to save his younger brother he remembers the teachings of an elder about building a portal to 'another world'. it's his only hope. He builds it and travels to the nether, where he finds his brother imprisoned in a nether fortress and frees him. But before making it back to the portal they are stopped by blaze guards. The guards call the older brother a foolish hero.... in netherspeak, "herobrine" For his feeble attempt to rescue is brother. The blaze then begins channeling a spell to banish him into the void -a forsaken place between worlds... Herobrine starts to fade "Help me brother, help me Steve!" Before the spell is completed Steve interrupts it and stabs the blaze in the heart. With Herobrine's voice fading Steve listens carefully.."Restore our world, kill the ender and nether dragon. Free our guardian and bring peace to our world. With our guardian restored it will break the curse on our people, they will come back, they will remember. But to aid their memory you must build something worthy of their return. You must....build the world. You must....save the world."Herobrine pushes Steve into the portal. Where he appears back in his once familiar land now void of anything his civilization has built and accomplished....and the only one who can save it.

Some extra details: There are two visually identical herobrines. One is Steve's true older brother. Though he cannot directly communicate with Steve anymore he tries to help him on his quest by manipulating blocks. The Ender Dragon created the second herobrine after finding out Steves real brother is attempting to help him. This second evil Herobrines job is to find Steve, trick him and kill him.
Creepers - They are search and destroy sentinel type creatures. Created after the banishing of Steves brother (Herobrine) who's real name is Joe and the escape of Steve out of the nether.The portals to the end In strong holds were created by elders between the sighting of the red dragons in the over world and the fight between the three dragon guardians. It was their attempt to travel to the end and kill the ender dragon, but they could not activate the portal in time.Only the Elders could read (this is why they saved the music and not books) I guess they knew they would eventually be found.
The testificates (non elders) only remember books as a form of decoration, which is why they still have them in their home. The fact that the normal testificates including Steve cannot read explains why Steve cannot read the enchantment table and has to randomly choose.Steve cannot fight the nether dragon now because it was wounded and in hiding somewhere in the Nether. this gives jeb or notch the ability to add a way to summon or find the Nether Dragon. Once the nether dragon is destroyed along with the ender dragon, it will free the dragon guardian of the over world. Their guardian will then free the elders from the skeleton curse, along with the people turned into zombie pigmen and endermen. Order will be restored and the people will have to rebuild meanwhile the guardian dragon is doing her job of keeping the monsters at bay and keeping peace.