There isn't enough information in your vague report to make any guess about the cause, and I'm not even sure what your subject line is supposed to mean. Obviously there's no malware in the simulator. It's kind of hard to hide malware when all of the source code is publicly viewable and you could easily build and run the client from source yourself.
However, to solve your problem, what you want to do is just force quit the program. How to do this depends on your operating system, which you didn't mention. If you are using Windows, open the Task Manager by right clicking on your task bar and choosing Task Manager (or press Ctrl+Alt+Del and choose Task Manager). Then go to processes, right click on javaw.exe, and choose End Process Tree. If you are using another operating system, please consult its documentation (or Google) for how to terminate programs.