Check your DMG for modern weapons. If you want more variety, modern armor and other equipment, grab them for free from the d20 Modern SRD. Modify the core classes to make them more modern. The NPC classes in the DMG are great for more mundane characters. Let your secret agents be Warrior/Experts; but let them choose if and how they multiclass. Add Drive and/or Pilot as class skills along with Craft (making secret agent items), Knowledge (secret agent stuff) & Profession (being a secret agent). Then, send them to rural Georgia to investigate a series of bizarre killings where they eventually encounter the son of Hogzilla, a giant dire boar--a story ripped from last week's headlines!
My point is that you don't need a bunch of new d20 material to run this kind of game if you want to do so. You can use your core 3.5 books.