Mega Man Battle Network has a linear storyline that does not have explicit divisions. However, the storyline can be divided by major boss fights. Completed areas can be revisited again. If at any point you are lost, you can press 
and MegaMan will give a hint on what to do next.
Unlike traditional RPGs, MegaMan does not have experience points, so he does not level up by fighting many battles. The only way to "level up" MegaMan is by collecting powerups. Even though many areas that you can jack into are optional, some contain powerups that make them worth visiting.
Managing your folder by replacing weak battle chips with stronger ones is important. Enemy viruses will have more HP and stronger attacks as you get farther in the game. You may also want to build your folder for the specific area you are in by using chips of an element type that counters the element type of enemies present.
Collecting battle chips is a big part of the gameplay, however, it is not necessary to obtain all of them to beat the game. In fact, some chips will not be available until after you beat the game.