1. Your a freaking superhero you can do what you want. Although if you do bad things you will be labelled a Villain and sometimes even when you do good things you'll still be labelled a villan (Take Spiderman when he just started for example). Anyways it doesn't matter if your good or bad depending how the Public sees your deeds you will have different encounters or missions.
2. Always check the mission board for new missions. I will be making missions for each hero or Organization however with the latter I will often just post it in the mission room of your base. These Missions will change with how you are seen by the Public so don't be alarmed if all of a sudden you are being attacked by good vigilantes when you thought you yourself was a good vigilante.
3. The Vigilante business is not for the faint of heart so if you fuck up. You will die. Not saying that I will kill people off for no reason but if your a Newbie and you are trying to fight a Superhero I will kill you off for just being stupid.
4. Often I will give out special mission which when completed you can get a new power or something else pretty cool. Anyways you will notice the difference as it will be green. Also if another PC vigilante is involved in the mission then it will be in red. If its a plot mission or something else extremely important then it will be in green.