I have a hard time getting what you don't get, but let's try
Say you have a game, with a nifty path-find algorithm that you don't want to fall in the wrong hands. Now you have 2 choices.
1. Implement the algorithm in javascript, and run it in the browser. Gives nice and speedy feedback. Player happy and cracker also happy, as he can just see how you did it, and copy it.
2. Implement it in whatever language at your server. Local browser has to send a request for a path to the server, server runs nifty algorithm, server returns computed path. Bit more slow, player still happy with nifty path, cracker less happy, as he only has input and output of the algorithm, and not the algorithm itself, unless he cracks your server.
You can also use this to avoid cheating.
Say you have a builder game, where you produce goods of some kind. It is precious stuff, and it costs time to make it, so a good target for cracking. Now you have (at least) 2 choices.
1. Implement the entire production in the browser, and send only to the server "I produced X amounts of goods". Player happy, and cracker happy, as he can send "I made a 1000000 stuff" every 5 milli seconds to your server.
2. Implement timing of production in the server. Browser sends only "production started at factory X", server sends "production ended at factory X, Y goodies added". Player happy, as he can still make goods, cracker less happy, as he can only send "started factory X", where X has to exist, and has no further powers to force the server into believing the production ended 5 milli seconds later.
Both examples move the actual game logic to the server, and only perform GUI interaction in the browser. A cracker may even fully implement the browser code by himself, but it won't do him much good, as game progress is under control by the server.
An extreme view is that the entire game is running at your server, where you provide a nice graphical GUI at the player machine as a bonus, since most people prefer to click at a tile, rather than typing "<productionstart time="56567467636"><factory x="21" y="54"><production type="foo"/></factory></productionstart>" for some weird reason