But where does the energy come from in the first place?
The battery converts energy from one form to another. A charged battery stores potential chemical energy (which is, fundamentally, electric in nature) and converts it to electrical energy by, if you will, "pumping" electrons through an external circuit.
Now, you may well ask "yes, but where did the chemical energy from?".
In other words, when you specify "in the first place", that's quite a chain to reckon with that, I suppose ends with the big bang.
First of all I recommend you to see in Internet Richard Feynman's WHY". It is exactly what he discusses, our questions about why.
An electron in an atom has two major types of energy, kinetic and potential. The first one is due to the fact that the electron performs a motion, e.g. if we calculate the average of the absolute square of the linear momentum of the electron in the ground state of a Hydrogen atom we find $< \hat {P^2} > \ = \ \frac {\hbar ^2}{a_0^2}$,
where $a_0$ is the Bohr radius.
The potential energy comes from the fact that between the electron and proton there exists an electrostatic field.
Now, why does the electron have a movement inside the atom? If the electron were localized at some time to a fix position, the uncertainty principle tells us that its linear momentum could have any value and it is not clear if the electron would remain in the atom.
Where from comes the potential energy: there are a couple of fundamental interactions with which is endowed our universe, and the e.m. interaction is one of them, see in Internet Richard Feynman's WHY. The types I recall are e.m. interaction, strong, weak, and gravitational. As Feynman explains, the existence of these interactions are fundamental axioms of our universe.
By what the energy in atoms (molecules) differs from other energies? Gravitational energy is due to just another type of interaction with which our universe is endowed. Strong interaction is what keeps together the components that constitute the hadrons (protons and neutrons) and the residual strong interaction keeps the hadrons together in the nuclei.
Best Answer
No, the car does (positive) work on whatever is stopping it.
Alternatively, you could say that negative work is done on the car, but still, the meaning is the same: the car loses energy and something else gains that energy. What that something else is, and what type of energy it gains, depends entirely on how the car is stopped.