The O'Neil family had been experimented on for generations by the Kraang (which included April's mom), as they needed to perfect the human DNA, so they would successfully be transformed with Mutagen in Earth's. This affected April the most, who exhibited unclear special gifts, which brought back the attention of the Kraang, who tried to abduct April, but got her mom, instead. She was then put into stasis in the Kraang ship buried beneath the O'Neil farmhouse.
April managed to distract Karai by revealing that she had also lost her mother, giving her time to escape.
Jack Kurtzman, a journalist who had been investigating kidnapped scientists by the Kraang, was the first to reveal to April that her mother had been captured by them.
The turtles find April's long-lost mother frozen in a Kraang ship buried under the farmhouse, though it's not really her, but rather a mutated clone with Mrs. O'Neil's memories.