The Prototype distribution is available from http://prototype.conio.net. The file prototype-x.x.x.js (at the time of writing: prototype-1.4.0.js) should be saved to a convenient location and renamed prototype.js.
Although Prototype can be referenced directly from the prototype distribution site, it is preferable and faster to work locally.
The following example assumes that prototype.js has been placed in a js directory and that the HTML file is alongside that directory.
The example shows a sample HTML file that uses Prototype and may be used as a simple sanity check.