Some TMNT stuff really isn't for little kids.
As a young boy Bruce Wayne was orphaned when his parents were struck by a truck containing mutagen. Spilled canisters of mutagen caused the mutation of Splinter, as well as four pet turtles that Thomas Wayne had purchased his son moments before, which Bruce named Donatello, Leonardo, Michelangelo, and Raphael. The grief-stricken Bruce was adopted by Splinter, and raised and trained in ninjutsu alongside the Turtles. As an adult, he fights crime as the Batman, with the help of his adopted brothers.
Along with his brothers, Batman fought the Smile Clan at the Natural History museum, where he fought the Laughing Man. During the fight, he was injured, and briefly saw his enemy as the Joker. Upon returning to their lair, he confided in Splinter that he was also troubled by recurring dreams where he was fighting alongside a human with black hair, and a sense of wrongness about the world.
This feeling was justified when the progenitor Raphael appeared in the lair and explained that their world was a combination of two different Earths, which served to weaken them all. Batman attempted to fight him, with little success, before listening to the story of what Krang was doing.
The knowledge that his life with his adoptive father and brothers was not his "true" one weighed heavily on Bruce, and he soon set out for the dilapidated Wayne Manor. There he found a disheveled Alfred Pennyworth, who recognized him from his youth. The encounter caused some of Bruce's memories of his parents' murder from the Prime Earth timeline to return. He then headed down to the Batcave.