In order to fully understand what an ion is, it's important to understand the structure of the atom. The structure of the atom was only discovered within the last one hundred years. It took many scientists years of hard work to unlock the secrets of these tiny particles.
As it turns out an atom contains a central nucleus which has protons and neutrons in it. Surrounding the central nucleus is a cloud of electrons. These electrons have an opposite electrical charge to the protons found in the center core. In a typical uncharged atom, there are an equal number of electrons and protons. Each positively charged proton is canceled out by one negatively charged electron. The electrons spin about the outside of the protons forming a type of electron cloud.
So what does all this have to do with ions? An ion is simply an atom that has an unbalanced ratio of protons to electrons. Due to the complex nature of atomic structure, it is sometimes possible to add or subtract one or more electrons to the electron cloud of an atom. When this is done, the imbalance of electrical charge causes the atom to become an ion. The chemical properties of an atom with an ionic charge are often quite different from those that are not charged.
Because atoms are so small they are virtually impossible to view directly. It is necessary to come up with a theoretical models that describe how they are structured. A major breakthrough in the description of atomic structure took place in 1909 with an experiment by a scientist named Ernest Rutherford. Rutherford hypothesized that an atom has a central core of very dense matter surrounded by a large amount of empty space. His experiment to demonstrate this is considered one of the classic experiments in the history of science.
Known as the gold foil experiment, Rutherford set up a very thin sheet of gold foil and shot a steady stream of subatomic particles at it. Ironically, these particles were actually ions themselves. They known to chemists as "alpha" particles, but all they really are is a hydrogen atom with its electron stripped away. Since all there is to a hydrogen atom normally is one proton and one electron, if you remove the electron, you end up with just a proton. An alpha particle is just a proton all by itself.
Rutherford found that most of the protons were able to penetrate directly through the gold foil without being deflected. This led him to correctly surmise that a vast majority of the content of an atom is actually empty space. The few alpha particles that did hit the solid nucleus were deflected at random angles. Most of them just passed harmlessly through the empty space of the gold atoms found between the nuclei.