Bat Brains have remained part of Robotnik's army during and after his rule over Mobius. They were redesigned after Robotnik began operating out of Flickies' Island, given a smaller size and more spherical shape. Despite the decrease in size, they were stronger and more maneuverable than the previous models and considerably more vicious. They attacked by dive-bombing, biting, or firing pulse blasts from their mouthes.
Since the New Robotnik Empire's invasion, both models have appeared, depending on the story.
- In Issue 39, a pair of Bat Brains attacked Robotnik (who they mistook for Sonic) by firing lasers from their eyes.
- Issue 1 - Enter: Sonic
- Issue 3 - Mayhem in the Marble Zone
- Issue 39 - Sonic No More
- Issue 42 - A Day in the Life of Doctor Robotnik
- Issue 43 to Issue 44 - Carnival Night Conspiracy
- Issue 45 - Day of the Death Egg
- Issue 64 - pin-up
- Issue 81 - Shock Tactics!
- Issue 89 - A New Hope
- Issue 99 - No Exit
- Issue 105 - cover
- Issue 105 to Issue 106 - Flickies' Island
- Issue 116 - Best of Enemies
- Issue 131 - Shady Characters
- Issue 131 - Game On!
- Issue 227 - R.B.R
- Issue 250 - The Battle For Mobius
- Issue 252 - Ebony & Ivory
- Issue 258 - Sky Chase
- Christmas Special 2012 - pin-up and cover
- Batbrain at Sonic News Network, the Sonic Wiki