Crazy wild theory! Squeaks is Ratchet placed in a body made by Cade. They recovered his spark from Lockdown's ship (Didn't Lockdown take his spark? I remember him taking something...) but don't have the parts to make him a proper body and don't want to place him in a drone/Lockdown's body, so Cade works with the Autobots to create a new body for him. Squeaks is basically like Baby Groot.