There are many ways to store energy. Capuchin is absolutely correct that you can't get back more energy than you put into the system in the first place (laws of thermodynamics). Near Niagara falls, they pump water up into a lake during the night, and then drop it down again through generators to generate power during the peak daylight hours. This is thermodynamically inefficient (energy is wasted), but economically efficient.
There are many proposals for getting hydrogen from water. In general, this involves putting a large amount of energy into water to generate hydrogen and oxygen. The hydrogen is captured and stored for later burning. The idea is to store energy for later use. Again, it's not thermodynamically efficient, but it works and it is useful and possibly will be more useful in the future.
It's technically possible to do what you're suggesting -- more or less. In particular, the storage part hasn't been totally worked out yet. Particle accelerators (linear accelerators, cyclotrons, synchrotrons, etc), strip electrons from any nuclei and keep the nuclei separate (usually in a ring -- but obviously at very low concentrations) as long as anyone wants them. It takes a lot of energy to contain them, but it can be done. It's fairly simple to add the electrons back in. Firing the nuclei at a charged plate would do the trick as these things are extremely reactive. The energy would be released as photons (radiation). The wavelengths of the radiation would vary. Quite a bit of it would be high-energy radiation in the x-ray or gamma-ray end of the spectrum.
The big problem would be getting the energy into a usable form -- electrical energy, mechanical, energy, etc. While it's possible to absorb photons and (for example) boil water to produce steam which would drive a turbine to generate electricity, these actions waste energy (laws of thermodynamics again).
So, the fundamental technical problems are 1) storage of a sufficient quantity to be useful (also remember that it would consume a lot of energy to contain the particles), and 2) recovery of the energy in a usable form later on.
Don't let the technical problems deter you from thinking about things like this. Although formidable, other technical advances may someday make this type of thing practical.
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