Rebuild an .exe as a Java package

i have some server files for an online game (silkroad),

and they all are .exe and infected

i want to make a clean, bug-free and virus-free clone of them that does the same job but in java for learning and experimental purposes and also i wanna run it on Linux

so the question is

if i have an .exe, how to look at it’s code so i can make a clone of it? or what are the available ways to do the task?

I’ve searched many times and found dis-assemblers and debuggers but this is gonna be pain