Prototyping is done during week 3 of Sprint 0, but note that many times existing feature enhancements skip the hi-fi prototyping phase. This is especially true if the development team already has a style guide for the product; when all the components of the feature enhancement are available in the style guide, there's no need to recreate them for a prototype when a simple wireframe will do. An example would be a layout change to a dialog - the components are already available and stylized, so the developers and QA only need a wireframe to show the new layout, organization, and interaction of the dialog.
There are as many prototyping tools on the market as there are wireframe tools, and the choice between them is again based on personal preference, company standards, and need. Some feature almost full blown development environments (iRise, Axure, Justinmind). Others let you build prototypes from code (Framer Studio, CodePen, Macaw), and still others are easy to use apps that are almost as powerful (UXPin, Proto.io, Protoshare). A nerdist hobby of mine is watching all the new prototyping and wireframing tools come to market and reviewing each. )Soon to be a set of blog posts.)
The best use for prototyping in hi-fi is to demonstrate to developers exactly what you want to have happen during any given page view or microinteraction. For example, if you need to show the exact speed a roll-up menu uses, these tools can do that, while wireframes and page-linked review tools cannot. Some examples of prototypes are shown below: