As Big Boss himself said, taking it all back to 0 solves nothing. As long as 0 remains, it will eventually become 100 again. But when you're Lex Luthor, skipping right into the thousands is all too easy, especially when you have a legendary hero doing the dirty work for you... err, Solid Snake is old? Guess Lex will have to change that... and what's this about the Joker?

In the deep vaults of Wayne Enterprises is the weapon known as Metal Gear Wayne; a weapon that absoloutely cannot fall into the wrong hands. As terrorists cripple Gotham, Solid Snake will have no choice but to team up with the Dark Knight to save the day.