I think you mean the Java quake 2 port, Jake2.
Either way, you won't be able to jump right in to things, especially if you're new to either C or Java. The Java port is almost a 1-to-1 rewrite of the original code, which doesn't fit with Java too well (everything is prefixed with the static keyword to pretend it's C). In short, I see no reason to base a game off it (look at JMonkey instead).
The quake 2 derivatives (warsow, dpball, etc.) are the superior choice.
However, you need to have some knowledge of the language you're working with before you plan this far ahead. Quake 2 is not among one of the easier engines to use these days.
Oh, yeah, it's
java, not
javascript.