In my headcanon, Penny´s friendship with Ruby caused a random script to develope in her core programming, and when she was killed, this random script transferred Penny´s soul to Ruby´s scroll. Now all that scroll needs s one hell of processing power so it can actually get Penny out of her dormant state, and then Ruby has a little cyber sidekick or something.

Man, if Penny would help Ruby upgrade Crescent Rose so Penny could help Ruby in combat, that´d be awesome. Penny could scan the opponent´s equipment for weakpoints and highlight them when Ruby aims at them, allowig Ruby to take down opponents much more skilled than her. Like, imagine if Ruby would´ve hit the barrels of Tyrian´s guns. They´d break and he´d have no ranged combat capabilities anymore. Or if she shot at the Nuckelavee´s mouth when it prepared another sonic attack (I mean, seriously, that´s combat 101: Hit where your opponent´s most powerful attack comes from when he prepares to use said attack and it´ll backfire on him).