Master Shenron is Omega Shenron after he absorbs all of the Dragon Balls in the galaxy, including the Black Star Dragon Balls and Namekian Dragon Balls. This is an alternative timeline. He takes on a new personality and a great amount of power.
When Goku and Vegeta had their energy restored by Senzu Beans, this enraged Omega. When someone mentioned other sets of Dragon Balls it gave Omega an idea, he absorbed all of the Dragon Balls in the galaxy. After that me found himself with more power then he ever imangined. Luckily someone had brought a living Gogeta and Vegito(who was already living). When he proved to be to much for them even when they worked together along side Ssj 4 Goku and Ssj 4 Vegeta, Gogeta and Vegito also had Ssj3. Gogeta suggested Fusion, the Fusion Dance and Vegito agreed to it. Master Shenron heard this and let them fuse leading to his destruction. After they fused he started to get pumpled but didn't care because he was holding back his true power. When he unleashed his true power he started to pumpled Vogeta, Gogeta's and Vegito's Fusion Dance fusion. Until Vogeta transformed into a Super Saiyan and defeated Master with one shot.