"Have Hacking, Mind Control and the Battery all active at once."
This achievement is not acquired simply by having all three systems (Hacking, Mind Control, and Battery) installed on your ship. In addition, this achievement is not acquired if you use Mind Control and the Battery while a Hacking drone is merely attached to the enemy ship. All three systems have to be activated and in use in order for the achievement to work.
Essentially, once all systems are installed and powered, enter a battle, deploy your hacking drone to an enemy system, pause, push the three buttons for the three corresponding systems, and the achievement unlocks.
This achievement is notably missable in a run if you've already installed all systems and either Hacking (Kruos starts with) or Mind Control (The Shrike starts with) is not among them, since you cannot uninstall systems to make way for others - besides the exclusive Medbay/Cloning Bay switch.