Isn't it obvious??!! The hyperdrive was just a...control box/organizer, per say, for mental energy the pilot put out to jump space. So, when Spensa finally found a way to 'unlock' that part of her brain, the hyperdrive triggered. Or..., maybe, since Doomslug can move WITHOUT Spensa seeing it, it can teleport. She has never seen an animal like Doomslug before, what if it came with M-Bot and the ship, in the compartment, and it makes the ship jump. So when it is signaled by the Pilot, from the screen, it teleports the ship to the designated destination. Spensa had a mental "shiver" right? So what if Doomslug picked up on her brain waves, saw what was going on, and teleported them out of there? It is plausible.