There's probably dozens of these around but to me some dont seem complete enough so i've done my own, it pretty much covers the basic importent parts of a safeguard mission and YES IT DOES CONTAIN SPOILERS so read at your own risk =)
Safeguard Guide
Okay in each mission briefing you are given an idea of which villain group is doing what and generally you will have two differet groups, one pulling the bank job and vandalising the neighbourhood and one generally helping out in the mayhem and getting in your way.
First thing to worry about is the bank robbery, now while most people panic and rush straight to the bank I will say "don't panic". The bank robbers are triggered when you get within a certain distance to the bank itself (flashing the sign telling you the bank is indeed being robbed).
In order to successfully complete the mission you must defeat ALL villains in the bank, this includes the small group standing watch just inside the doors (usually three minions and a leuitenant) as well as the named villain and his mate. Now while you are fighting the first group the villain is attacking the vault door (unless in some cases they are taking their time for some reason) but you may get the "The robbers are getting away" sign flash up.( Its also wise to note if you are defeated at any time, going to the hospital will take you back to the mission starting point so you dont leave the map at any point)
Again, don't panic. If you are hard pressed back to a doorway you know the bad guys have to come through, or if you want an advantage wait for them outside. If you at least aggro them in any way you will disrupt their flight as they will attack you, if you miss at least one of the group in the bank then its a chase to their get-away vehicle to stop them (meaning a possible fight with some along the way, escape point is also marked on the mini-map), if one gets away you fail, doesn't matter if you get the main bad guy or not.
When you complete the mission thats when the real fun begins, vandals begin to show up at different periods to wreck scenery and make mischeif, backed up by the second villain group who are hanging around to take advantage of the mayhem. Defeating all in a vandal group gets you one and a half minutes added to your timer (which begins at fifteen minutes), again the key is to not panic, at lower levels the vandals don't do too much damage to make a difference to your timer to really care to start off (if they do too much you lose time) The real fish are scattered around your map in the form of side missions.
Side Missions- These are just as thier name suggests and their benefits range depending on the mission received. The Key to each mission lays with a group of the first villain group (the ones pulling the bank job along with the named villain) who are doing something to give away the type of side mission (e.g arson side mission you will see one of the group holding a molotov cocktail, etc) defeating all in the group will earn you the key to the side mission and a chance at more time and rewards.
Arson- This is a basic "beat the baddies and disarm bombs" mission you need to complete in a set time, there is a second group waiting inside after setting up their bombs so you will need to defeat them before dealing with the bombs, be quick as you will get an ambush come in while you are defusing the bombs to try and disrupt your attempts. The only reward I've gotten is the extra time added to my timer.
Building Bombing- Again a basic "defuse the bombs" mission set in a sewer/cave/building map where you must defuse four bombs, defeating the villains isn't important to complete it but you will find they do annoy you as you look for the bombs. Again the only reward I gotten was added time.
Weapons Deal- This is a "find the glowie" task in a warehouse map, you can either fight your way through the baddies inside or sneak past, either way will work and depending on the time remaining is how you should proceed. Main thing to remember is as soon as you enter the building watch your back as an ambush will follow you into the building (annoying while soloing, deadly with a team effort). Rewards are added time and a temporary weapon of some sort. (randomly determined) Ive found sometimes the temp power isn't given, I'm not sure if this is a bug or Ive already gotten the temp power before.
Break In- Another fun one where you enter the shop to fight off the theives before they break through to the vault. First thing to do is save the hostages (the attack on the vault only starts when you show up at the vault) bonus for rescuing all four hostages is a random DO/SO matching your origins but you need to rescue the hostages, not prevent the vault break-in, time is added for preventing the break-in itself.
Jail Break- Inside the police station there are three police officers being held at bay, defeat the groups around them and they will help you out (becoming pets for the remainder of the safeguard mission) also in the prison area is another named villain and friends to stop, defeat this group to complete the side mission. Time and gaining pets are the reward but be warned, as you leave the police station there will be two ambushes from withn the station and three groups (at least it feels like three) will come at you from outside so chances are you might lose your pets if youre not too careful.
One very important thing to remember is while you are doing the side missions don't get the urge to run off when you see the "vandals causing maynem" sign flash up, the time gained from a side mission more than makes up for anything they destroy.
Once you have the time from the side missions deal with whats left at your leisure the rest of the mission is just a fight for experience and influence.
Those of you seeking badges I will say the nine times out of ten a badge will be near either a side mission or vandal spot (mostly the ones I've got were me accidently running past them as I fought) but there are websites giving locations.
If ive missed anything please feel free to add on but apart from this relax, don't panic and enjoy protecting the banks of Paragon City.
Only three? It sure seemed like about 300... We spent what felt like 200 years fighting off foes, it finally looked like it was done, we started to go in, and BAM! More came. Happened about 5 or so times. I think we spent at least an hour fighting the ambushes.