Some of this information can also be found in the official strategy guide. [divider]
There are two main factors that influence the difficulty of a mission in PvE: the level of the mission and the Skulls active for that mission.
Mission level is set to a certain baseline for Story missions and Strikes, but once you hit 20, all missions can be scaled up to (and beyond) Level 20.
There is also a special set of Vanguard Strikes that allow you to play a random Strike at Level 18, 20, 22, or 24.
Two Skulls in particular serve as a sort of mission-wide difficulty setting—the Heroic and Epic Skulls.
On Heroic, encounters are changed, and all enemies are more dangerous.
On Epic, the encounters are changed, adversaries are yet more dangerous, and an additional enemy combatant for each race in the game gains a new elemental shield. On top of that, elemental shields take 50% less damage if you hit them with the wrong element.
The difficulty tier for a mission sets the base level of aggression for all of the enemies in a mission. This affects how fast, accurate, and dangerous the basic foes you encounter are.
Also, all adversaries improve their basic behaviors: dodging your gunfire, diving away from grenades, suppressing you in cover with weapons or grenades, flanking you, chasing you behind cover, rushing you in melee, hiding and retreating to recover shields, or jumping away if suddenly ambushed. The specific behavior depends on the exact enemy type you are battling, but all of them are more dangerous on higher-difficulty missions.
Majors and Ultras
Majors and Ultras are the special hardened versions of normal enemies that you may encounter during a mission.
Majors show up with a yellow nameplate. They have more health, possess stronger shields that recharge faster, and are more aggressive and dangerous than their normal brethren. You may see these foes show up in the game with a name like “Elite Fallen Captain,” but you can always identify them by their nameplate color.
Ultras appear with a skull mark on their nameplate. They are tougher still than Majors and more dangerous, and all of them have a 360-degree knockback to push you away if you get too close.
Enemy Behavior
The difficulty tier for a mission sets the base level of aggression for all of the enemies in a mission. This affects how fast, accurate, and dangerous the basic foes you encounter are.
Also, all adversaries improve their basic behaviors: dodging your gunfire, diving away from grenades, suppressing you in cover with weapons or grenades, flanking you, chasing you behind cover, rushing you in melee, hiding and retreating to recover shields, or jumping away if suddenly ambushed. The specific behavior depends on the exact enemy type you are battling, but all of them are more dangerous on higher-difficulty missions.
Skulls
Skulls act as special difficulty modifiers for PvE missions. These added effects are on top of the basic difficulty for any mission in the game at any level. If you tackle a Strike that is three levels above you and has multiple Skulls active, expect a very, very tough fight.
Special daily and weekly missions can often have Skulls active. You can also adjust the difficulty on a mission to change its level and sometimes the Skulls that it has active.
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During a Nightfall mission, if your entire Fireteam wipes, you are returned to orbit instantly. You only get one shot at these missions, so play smart!
By completing the Weekly Nightfall Strike, you’ll receive an XP bonus until the weekly reset and blue flames for the duration of the bonus!
[divider] If you were wondering about some of the recent Destiny stats, this cool infographic from DestinyDB gives us a lot of interesting information about Destiny’s players: