An EXE is a compiled program. If you don't have the source code of it, there's really no way you can modify it. If there would be a way, we wouldn't have to make Plus! hook into Messenger but simply add its source to Messenger's...
Also, it would make programs very vulnerable for malicious programs. Think about a script which changes a virus scanner's code to make it install virusses instead of preventing you from them.
The best way to make your idea is by developing such program by yourself, or asking for the code from the original creator.
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