Then it moved to a Flash version. If I remember right, this was at least somewhat motivated by vendors dropping Java support in the browser. Of course, at almost the same time the Flash version came out, vendors started dropping support for that.
The current one is written in JavaScript, I believe. Edit: it's still running Squeak, but using a JavaScript Squeak interpreter. See the top-level site for the given link.
TFA isn't the current version of Scratch. It's Scratch 1.4—which was written in Smalltalk—running in a browser via Squeak.
If you've used modern Scratch, it's interesting to see what has changed (and what hasn't).
This motivated the MIT guys to port Scratch to Flash (very bad timing) and the ex Squeak guys to focus on Javascript (Lively Kernel and other projects).