Disclaimer: It's been a while since I've run Mutants and Masterminds. Since then I've played at a convention, and I've made characters, but I have at least kept up a bit with M&M 3rd edition, and I've even made up a character that I've yet to play in a friend's campaign, because life is a complicated thing when it comes to adult schedules.
I'm fairly certain I've discussed this before, but one of the things that never quite went right for me with my group was using hero points as a GM to just explain how a scene resolved. The first time I tried to do it, I just had players say "we don't want the hero points, so the bad guy doesn't escape."
Now, that's not really covered in the rules, but I'm fairly certain the assumed way this is suppose to work is that you trust the GM enough to just fork over the hero points for you, and the bad guy escapes, your weakness incapacitates you for a few rounds, etc. Nobody has to jump through hoops to look up rules to make the scene work the way it would in the comics, because it's not a back and forth combat round or skill challenge that is going on.
Similarly, it just always felt a little loose to hand a player a hero point so that my bad guy could re-roll to hit that hero, or to resist the hero's attacks. On top of that, handing a player a hero point when you know the night is almost over just kind of feels wrong, like paying them with currency that won't be valid in a few minutes.
After having played a lot of Marvel Heroic Roleplaying and having read and played a little bit of Fate, I have to agree that there is something a bit more "cooperative" in the way that those systems handle "GM edits," situations where the GM pretty much just throws the player's agency out the window. You can do anything you want with your 2d12 in Marvel Heroic, but you have to wait until you have "earned" those d12s in your Doom Pool. In Fate, the players have the option of spending their fate points to cancel out the things that you want to do, so that it becomes more of a discussion about how the scene should play out, and even if there is still a hint of the adversarial in paying the GM to cancel out his "gotcha" moment, there is an economy involved that means the player isn't completely without some say in what's going on.
So with all of that in place, if I were running Mutants and Masterminds again, here is my spin on what I would do with hero points.
How Many Hero Points Can I Have?
Default Mutants and Masterminds 3rd Edition assumes that you can have any number of hero points per session, but that they always reset to 1 hero point at the beginning of the next session. This means that handing out a hero point at the end of the night towards the climax of the big fight, when your character might not even get another turn, is kind of a let down.
Under this system, you can bank your hero points, but not indefinitely. The game really wants you using those hero points, so you lose 1 hero point each session, until you reach a minimum of 1 at the beginning of the next session.
It still means that you might get a little bit of a lackluster extra hero point at the end of the session (hooray, I have two, and we're 10 minutes from the game being over), but it does mean that those nights where the GM put you through Hell (perhaps literally) and you earned 6 hero points that you never got to spend, because you were rolling phenomenally well for once, won't hurt quite so bad, because next session you start with 5.
The GM Wants to Do What Now?
Any game system will ask you to have a certain amount of trust in the GM. If the GM always intended the bad guy to have backup showing up in 10 minutes, you have to trust that the GM had that planned. On the other hand, the GM has to own up to the idea that he wants his bad guy to escape without giving the players a chance to catch him, or that he wants to use one of the PC's weakness against them but not stat out that weakness in game terms, and just describe what happens.
In addition to the above "GM shortcuts," the core Mutants and Masterminds rules assume that you can have your bad guy essentially get the effect of a hero point by paying a hero point to the hero effected by that decisions. So if the bad guy is re-rolling his attack on a PC, or re-rolling his check to resist the PC's attack, stand M&M logic would be to hand that player a hero point.
Taking a page from Fate, if the GM wants to introduce one of the above complications, the GM offers the player a hero point (if the complication effects multiple players, he offers each of them a hero point). If the players do not want to accept the GM's complication, they can instead hand over a hero point to the GM to cancel out the complication (if the complication effects all of the PCs equally, each player has to hand over a hero point).
Now, this does mean that once you don't have a hero point to pay the GM, he can introduce a complication with impunity, but then you have a hero point again, and on top of that, it gives you incentive to earn a second hero point just in case you want one to cancel a GM complication in addition to being able to do more of the player facing things a hero point allows you to do.
All New #1 Issues!
Sometimes, the GM wants to assume some time has passed. It's been a year since the alien invasion, or six months have gone by since the first super hero on the planet died saving his home city. You want to refocus, ask the players what they did in all of that downtime, and start from a fresh new point for the next phase of the campaign.
Whenever that happens, all hero points reset to 1. In comic book terms, it's great for for the hero points you built up to carry over from one issue to another when you in the same "story arc," but remembering how warm and fuzzy saving that kind from the apartment fire six months ago when you and your team have ended up traveling to an alien world in order to stop a planetary civil war probably doesn't make much sense.
As the GM, you shouldn't be doing this every game session if you are using the above rules. Try to think of it in terms of comic books. If it's been a month or less since the heroes did what they did last session, they should probably still have all of their hero points intact, unless there was some dramatic events that changed the whole feel of the campaign over that month's time.
When in doubt, bring the player's in on your decision making. Tell them that the next story arc is removed from the previous one by a good space of time and you think it makes sense to reset your hero points. Most of the time, the group is probably not going to have a hard time with this.