Agent is the game's lowest difficulty. Guards are inaccurate, weak in both damage and health, and have slow reaction times. Bond also has much less in the way of objectives. There is usually additional body armor available on this difficulty. Weapon pickups will increase your spare ammunition count the most in this difficulty. Auto-aim works well.
Secret Agent is the game's medium difficulty and usually has more objectives than Agent but less than 00 Agent. The guards are also improved, boasting more health, damage, accuracy, and reaction times. Weapon pickups will replenish slightly less ammo. Secret Agent also removes some locations of Body Armor spawns from Agent difficulty. Less effective auto-aim than Agent. This is not the case in the Japanese version of the game.
00 Agent is the hardest of the game's three preset difficulties. There are more enemies in general, and have the greatest stats out of all the difficulties (sans 007 mode) and Bond has more objectives to complete than on other difficulties. Body armor is usually scarce or nonexistent on most levels. Weapon pickups will replenish your ammunition count the least amount in this difficulty. Larger explosions can easily be fatal, and can take off more than half your health in a single hit. Auto-aim function is almost non-existent. However, like with Secret Agent, this is not the case in the Japanese version.
007, often referred to as "007 Mode" or (less commonly) "007 Agent", is a special difficulty unlocked after completing every mission on 00 Agent. It is something of a sandbox mode, allowing the player to set the health, damage, accuracy, and reaction times of enemies before starting a mission. It is generally designed to increase the re-playability of the game; applying the extreme high and low settings will far outstrip the difficulty presented by 00 Agent and Agent respectively, and thus 007 Mode can be used either for an extreme challenge or simply for fun.
007 uses the same objectives and object placement as 00 Agent, although the framework does exist to allow it to have its own. The weapon pickups will also only replenish the same amount of ammunition as if you were playing the 00 Agent difficulty. Auto-aim works quite well in 007 mode.