After you defeat the Creator, there is a looooooooooooooooooooooooooooong epilogue, including the rolling credits. Wait for the credits to finish and there will be a cut-scene, after which you'll regain control of Lea. At this point, the achievement will pop.
Be patient - like, really patient - and don't exit the game. Looking at my achievement unlock times, it took 22 minutes from when I beat the Creator until all the scenes and credits were done.