To avoid being killed by the emperor, Rain betrayed his homeland and joined Shao Khan's forces as one of his assassins.
Before the events of the original Mortal Kombat game, Rain was smuggled away from his homeland by his father when Shao Khan invaded the realm. After Shao Khan took over and killed his father, Rain stayed hidden for thousands of years before being discovered during the events of MK Trilogy. In the series' original timeline, Rain was the son of Argus, Edenia's godlike protector, and was sent away to live with a human general of the Edenian army while unaware of his true heritage. Rain, a purple palette-swapped ninja named after the Prince song 'Purple Rain,' appeared in Mortal Kombat 3's arcade attract mode, fueling speculation that he was an unlockable of some sort, but he wasn't actually in the game. Like many MK red herrings, Rain would eventually become a playable character with a full backstory in the UMK3 update, Mortal Kombat Trilogy. During the 2D Mortal Kombat era, the series became infamous for inserting red herrings in each game, such as fake characters meant to trick players into thinking they were unlockable. Rain's first appearance was actually meant to be a joke.
