This game may not be the hardest in the series compared to previous games... but these levels might make you think otherwise.
- Mission 6 - Long Day. It's an Annihilation mission, meaning that players must cause enough damage to enemies to exceed a certain score threshold within a time limit for the mission to be successful. The actual opposition in that mission isn't terribly challenging, but the threshold for points is high and the time is low, and causing enough damage to pass that threshold using only the options available to a player early in the story is quite difficult, especially if they are playing through on Hard difficulty. However, the mission becomes much less arduous (and far more enjoyable) on subsequent playthroughs with better planes, and even a sizable number of first-time players have expressed similar opinions while flying in A-10Cs (or higher-tier aircraft like the Su-34, provided the player has enough MRP at the time).
- Mission 7 - First Contact. You're destroying enemy SAMs and radar sites in a twisted maze of canyons under extreme weather conditions, which only get worse in the latter part of the mission, where you're fighting the fast UCAVs and enemy aces in a lightning storm with barely any visibility.
- Mission 8 - Pipeline Destruction. Your mission is to destroy the Erusean fuel factory. The objective itself is simple (and fun), but the latter half of the mission involves tracking down fuel trucks, which are fleeing under the cover of an absolutely brutal sandstorm that can send your plane into the ground and completely hides the trucks from radar unless there's a gap in the storm or you get within about one kilometer/half a mile or so of them, meaning you're basically flying blind while feeling around for them. Further complicating matters, during the sandstorm, Erusea looses a swarm of MQ-99 drones to hunt you down. And just to complicate the No-Damage Run medal, some of the fuel trucks are actually carrying strange blue high explosive devices that hurt you if you're caught in the blast, something that the player may have only noticed in passing during Mission 2.
- Mission 9 - Faceless Soldier. In the first half of the mission, you must fly below the clouds in the narrow canyon. Stay above it for too long, and you'll get shot down by invisible SAM sites that launch high-speed projectiles that can't be dodged or spoofed. It doesn't help that the mission targets you're required to destroy are often located above the clouds, forcing you to fly up in order to strike and hurry back down, where you could crash into the ground because you never know what's waiting below the clouds. The real kicker is that the topographic map in the radar can be deceptive, a player might be forced into a cul-de-sac valley, try to quickly rise over the mountains at the end to dive into the clouds on the other side, only to find that there is no cloud cover on the opposite side and no time to turn back. Fortunately, the second half of the mission is a glorious turnaround. It is also very hard to S-Rank, compared to other levels. The situation only worsens on Ace difficulty, where the missile alerts become nigh-instantaneous the moment you fly above the clouds.
- Mission 12 - Stonehenge Defensive. While it is an excellent mission, it can be frustrating to S-Rank, mainly because it initially starts as a ground attack mission, with heavy amounts of ground targets (favoring an Attacker-type plane such as the A-10C)... only to swing heavily towards being primarily based around aerial combat halfway through, with heavy amounts of bombers, enemy attackers and fighters, topped off with the Arsenal Bird and its 80 MQ-101 UAVs, meaning going into the mission with a plane geared towards one or the other will make it difficult to destroy all of the enemies. Additionally, the mission requires frequently jumping from one side of the map to the other, as enemy groups spawn in various locations far from each other, necessitating a fast aircraft. This also makes the mission far less fun to replay, since the number of aircraft success is even feasible with is highly limited, discouraging experimentation with anything other than certain multirole planes... or the F-22A Raptor, as usual.
- Mission 13 - Bunker Buster. The main gimmick is the bunker buster's laser targeting system, which replaces the SP weapon slot. It is rather difficult to aim the laser and there is a delay between calling in the bomb and having it land on the bunker. Factoring in the presence from the enemy planes and gun encampments, the presence of fake silos and the strict time limit before the ballistic missiles start launching (which will result in having to chase down more than three missiles if you can't destroy the five bunkers in time), this mission can be quite the headache.
- Mission 14 - Cape Rainy Assault. The first part of the mission involves a somewhat lengthy canyon flight that involves dodging searchlights. Then comes the assault on the airbase, which can be surprisingly difficult as there are many airborne and ground targets that need to be destroyed within an extremely strict time limit that is much shorter than the official mission timer would have you believe, or else the allied ground tropes will be overrun, with very little room for error.
- Mission 15 - Battle for Farbanti. The threshold for points is quite high, the time limit can be somewhat restrictive, there are lots and lots of enemies spread out across the whole map, and it is difficult to S-Rank, partly because the dogfight with Sol Squadron and Mister X in the second half can drag on for a while.
- Mission 16 - Last Hope. Due to circumstances at the end of the previous mission, your IFF systems are inoperative, so you have to manually identify your targets by flying close to them and keeping them in your field of view; this process can be slightly sped up by locking into a target and focusing the camera on it. Oh, and don't expect to leisurely learn this new mechanic in a simple offensive operation. This is the last Escort Mission in the game, and a doozy at that: Your escortee is an ordinary car with the offense and defense you'd expect of one, and it's so slow by aircraft standards that attempting to match speed with it will just stall your plane. You have to weave your way around a metropolis with many tall buildings, taking out any AA installments and aircraft that threaten your payload, while making sure to ID them first (and hope they don't shoot down the car while you're scanning it), as the mission will be marked as failed if you shoot down too many "Unknown" targets, even if they did turn out to be enemies. Then, once you're past that, you have to escort a different vehicle; thankfully, it's an airborne one this time, but this particular escortee has the twist of being marked as an enemy vessel (i.e. with a green reticule) despite not being hostile, meaning you can easily fail the mission because you didn't check who you were locked to before firing your missiles.
- Mission 17 - Homeward. The LRSSG are attempting to re-locate to Tyler Island, and to do so they must wipe any Eruseans off the map. Simple Annihilation mission, right? LOL. Again, there is no IFF support (Kessler Syndrome and all that), so, as with Mission 16, you have to ID everything before you shoot it. IDing a target takes significantly longer than just shooting it, which limits your DPS. You are then interrupted by a Timed Mission in which enemy bombers approach the island to commit a saturation attack; there is heavy cloud cover from the east, complicating any sort of interception. You still have to ID all your targets, meaning you have to move fast and shoot straight while fighter cover tries to stop you and without TGT tags (which only get added after you ID something, at which point you might as well just take an extra few moments and shoot it down). If any of them pass the threshold, it's a Non Standard Game Over. And remember, this is an Annihilation mission, so we're talking Checkpoint Starvation: if you mess up, you start over. Then it's back to the island, until a Cut Scene and a checkpoint. After this is another Timed Mission where you have about 90 seconds in which to destroy certain enemy units that are besieging an allied position; the game doesn't mark the relevant units with TGT tags. (At least AWACS Long Caster IDs everything for you.) Finally, there's another checkpoint followed by a high-speed interception mission as you chase Single-Stage-To-Orbit spaceplanes that, depending on your mount, could possibly outrun you. Through thunderclouds. None of these tasks are particularly difficult by themselves, but the fact that you have to do them together, all in a row, without a return line, with additional fail states in every segment of the mission beyond the standard hazards of crashing or getting shot down, takes it over the top.
- While the Season Pass missions usually combine fun with a bit of challenge thanks to the multitude of targets, the same cannot be said for SP Mission 03 - Ten Million Relief Plan, which will punish you dearly if you're not adequately prepared for it. The first section is a boorishly long Escort Mission that requires you to cover a really wide area to intercept SLUAVs and SACS Rafale Ms that constantly dodge your missiles, made worse by Wiseman's utterly idotic decision to have the LRSSG uselessly follow you around (and sometimes take away precious targets from your score) instead of spreading evenly to protect every Specter plane, whose F/A-18F escorts are just as nonexistent. Then comes the boring MAD section where you're forced to fly at low speed and altitude to detect the Alicorn. Then comes the big submarine fight, where you have to deal with an insane amount of missile launchers, railguns, jammers and even barrier drones that act like the Arsenal Bird's APS. Overall, the contrast between the lethargic sonobuoy section and the absurdly action-packed Alicorn fight is just too much to warrant any sort of replayability.