I am not using any special tools. HxD is a free hex editor. At first, the data in a Starfleet executable looks totally meaningless -- just a bunch of stuff like E9 E2 04 00 F0 E2 08 00. [Shrug]
But then you find gems like this: 09 08 07 06 05 05 04 03 02 01 01
What is that?
If it were 09 08 07 06 05 04 03 02 01 00, it could be a count down, a list, or anything generic. But the former series is far too specific to be anything random.
You need to learn how to read numbers in hexadecimal form. (It temporarily hurt my brain learning this!) If you're looking for a ten, that may be written as a "0A" byte. (It may be written as "0A 00 00 00" for a 4-byte integer. Why not "00 00 00 0A"? That's little-endian format. Yes, another brain twister to resolve.) The Windows calculator in programmer mode can do part of this for you, once you understand the concept. HxD has a search function that finds little-endian values.
Let's say I want to find the damage that Large Drones do. That's 24, right? I need to search for 24 in hexadecimal format. That's 16 plus 8, which is "18" in hexadecimal (don't say eighteen, say one-eight). But if I search for "18", I'll find several thousand of them! I need to be more specific and use the clues that are found in human-readable hex. And also try 4-byte (32-bit) values like "18 00 00 00" which greatly narrows down the search.
Scattered throughout the .exe are strange words like AVtDrone, AVtPhoton, AVtHellbore, etc. These can be helpful indicators of what's nearby.
I began exploring the Starfleet2CE.exe because I wanted to fix the misleading version number in the splash screen. 2.6.6.0 was wrong, it should be 2.6.7.0. Okay, I found that 7 times in the code! One of them must affect the splash screen. Trial and error found the relevant address to be 0065FA28. You can change 2.6.6.0. to A.D.A.M. if you want. (Use the human-friendly right column of the HxD screen to more easily change alphabetical stuff.)