All of these agents are really confuzzling me with this virus stuff I haven't seen the Matrix...

It's not that hard The Matrix is all about we living in a computer generated world. There are some "freed" of that world, and live in the Real World, but have still access to the Matrix. They can do remarkable things in the Matrix, because the Matrix is based off rules, which can be broken or bent. That's why they can be fast and such.
Well, then there are the Agents. They are programmed to destroy those who are "freed" of the Matrix, because they are a threat to it. Agents are overall much better than those who are "freed", so usually you'd better run if you see an Agent.

And the virus thing.. well Agent Smith once said humans were like viruses. We act exactly like them. We go to a place, multiply ourselves, use all the resources available to us, and if we cannot live anymore on that place, we leave it be, it's as simple as that. That place will never be what it used to be.. And then, we move on to the next place to ruin it. I can see some truth in it, but it's not fully true, though.

I hope this explained it a bit .