For server side debugging, you'll need to use a tool like Node Inspector. Before you get started, check out some of these useful tutorials.
tl;dr - there are a number of utilities in the Meteor ecosystem which are designed to be run at the same time as your Meteor application. They only work if your Meteor app is up and running and they can connect to a running website. meteor mongo, Robomongo, Nightwatch... these are all utilities that need your application to already be running. NodeInspector is one of these utilities.
# install node-inspector terminal-a$ npm install -g node-inspector # start meteor terminal-a$ NODE_OPTIONS='--debug-brk --debug' mrt run # alternatively, some people report this syntax being better terminal-a$ sudo NODE_OPTIONS='--debug' ROOT_URL=http://myapp.com meteor --port 80 # launch node-inspector along side your running app terminal-b$ node-inspector # go to the URL given by node-inspector http://localhost:8080/debug?port=5858