So, Pokeballs. Those familiar things that shoot red beams at Pokemon, make them red, and suck the whole thing in. If you look closely, they're also those familiar things that have shiny metal plates on the inside. I believe that the Pokeball contains a harsh version of an Alpha particle beam. Confused? Well, a particle beam is essentially a laser beam. Light (which includes all light, not just the type we can see) exists in both particles and waves. Taking this, we can measure the intensity of a type of light (say, an X-ray) both by how closely spaced the waves are and by how much energy the particles of the light contain. Understand the particle beam part? On to the last. There are about three main types of high-energy light beams; the Alpha, Beta, and Gamma rays. The Gamma ray has the highest amount of energy, the Beta lesser, and the Alpha the least. Remember that though the Alpha beam has the least energy from the three, it still has a lot of energy. Keep in mind.
So, back to what I was saying. This Alpha particle beam stays inside the Pokeball most of the time, since, when it tries to go out, it just gets reflected by the metal plates lining the inside of the Pokeball. But when the circle in on the Pokeball gets pressed, that circular piece of metal retracts, and the beam has a path to go out through. It hits the Pokemon, and then a complicated thing happens. When the beam touches the atoms of the Pokemon, it transfers all its energy to the electrons. All the electrons seperate from the atoms, and the atoms go into the surroundings. What you have left is a blueprint of the Pokemon. You must have learnt that each substance has atoms with different numbers of particles? This makes use of that fact. As soon as this has happened, the air inside the Pokeball is given a lot of protons, making the air have a positive charge, and the electron 'blueprint' - or, as I like to say it, Winzip file - is attracted back into the Pokeball in that position. Later, when the electrons are released again, they immediately attract their respective kinds of matter towards them, and the Pokemon is reconstructed from that Winzip file.