Additionally, following it through will alter critical game files. Be sure to make back-up 
files of the files you are altering, or be ready to re-install the game. If you have no 
idea what you're doing, or no idea what we're referring to/talking about, do not attempt 
this hack. 

Locate the directory C:\Program Files\SEGA\Alpha Protocol\APGame\Config\ 
(this is default install path). 

Find and back-up the file "DefaultLevelChart.ini" into something like 
"DefaultLevelChart_ini.BAK" or "DefaultLevelChart_ini.BACK". 

This is the file where you will find the AP points you will have, as well as the skill 
cap maxima.
An example syntax is:  LevelChart(MinXPNeeded=0, APGained=30, SkillCap=4, SpecialSkillCap=4)

Alter it to something along the lines of: 

 LevelChart(MinXPNeeded=0, APGained=500, SkillCap=10, SpecialSkillCap=15) 

With the above example, you will now get 500 AP points and can max out to skill cap below 
special skill level. Be sure to save the file as a *.INI file (Notepad will generally allow 
you to edit INI files) and not as a *.TXT file. Boot the game and wreak havoc.