First add the "upstream" remote:
git remote add upstream https://github.com/mrdoob/three.js.git
Then fetch it:
git fetch upstream
Merge it with your local code:
git merge upstream/master
Resolve any possible conflicts (i.e. go through each file and edit it as necessary), commit and push them, and you're done!
Hopefully the network graph will show you a nicely updated graph in your timeline ;)