Opening Mission

The online mode is named MGO, not MGSO. And Metal Gear Solid Portable Ops is called MPO. It really stands for Metal Gear People Online, meaning it's everybody's Metal Gear. 気持ち悪い? "P" is really "p"eople's "P". You don't just play with your friends, but you play with everybody. You play with "Metal friends". That's what MPO represents.
Like it often happens in the world, for political reasons, The Boss was used. The Boss being used this way, is it considered justice, is it the righteous path, it is certainly being interpretted that way, and that's how it was concluded.
But to Big Boss, or Naked Snake, losing The Boss, he isn't going to accept it, and he can't make peace with the organization that allowed this to happen, nor himself for allowing it to happen, so he runs away from FOX. That's why the mission in MPO happens. It starts off with Snake being captured.
This is the time when Big Boss created Outer Heaven.
This is when Big Boss first meets a young Roy Campbell.

Campbell and Snake's encounter, of course, is mirrored in MGS4. In 4, Campbell also encounters Snake, even though it is not Naked, even though it is Solid this time, Campbell's constant feelings of nostalgia toward Solid Snake is really rooted in his relationship with the original, with Naked.
There is another bigger reason behind the meeting, but that will have to wait until the game's release.