I tried looking it up, and according to Wikipedia (not a scholarly source, but there it is), there are in principle several ways you could do it. A lot of disappearing inks use Thymolphthalein, which changes color as a function of pH - in neutral or acid solutions, it is colorless, but it turns blue in basic conditions. How you douse your paper in acid or base I don't understand (paper doesn't like to get wet, after all). Other disappearing inks I'm sure use a similar basic principle, namely a compound that is colorless or not depending on some kind of environmental condition.

Wikipedia has a good little section on disappearing inks in its article on invisible inks:

"Inks that are visible for a period of time without the intention of being made visible again are called disappearing inks. Disappearing inks typically rely on the chemical reaction between thymolphthalein and a basic substance such as sodium hydroxide. Thymolphthalein, which is normally colorless, turns blue in solution with the base. As the base reacts with carbon dioxide (always present in the air), the pH drops below 10.5, and the color disappears. Pens are now also available that can be erased simply by swiping a special pen over the original text. Disappearing inks have been used in gag squirtguns, for limited-time secret messages, for security reasons on non-reusable passes, and for fraudulent purposes."

So, disappearing ink turns colorless after it reacts with carbon dioxide in the air, which turns it from a colored ink to a colorless ink because of an acid-base reaction.