Missions (Long War)
Standard Missions
Alien Missions
Alien Abductions
Alien Abductions are generated by landing UFOs - the UFO will disappear and be replaced by an abduction site that you can respond to, even if you don't have that country covered and didn't detect the incoming UFO. Shooting down the UFO before it lands will, naturally, prevent the abduction being generated. Due to the different format, abductions will only affect one country at a time and you no longer have to choose. The reward for abductions is always credits. Skipping or failing an abduction mission will result in increased panic in the affected country and continent.
UFO Crash Site
When a UFO is shot down and not destroyed, a UFO Crash Site mission becomes available. Completion of a UFO Crash Site mission rewards the player with the possibility of recovering valuable components from the UFO--- however, a crashed UFO is now even more likely to have destroyed artifacts. In fact, after the first round, you will more often than not hear the UFO's Elerium Generators exploding. Be forewarned some UFOs are crewed by elite crews; these will have a large number of strong aliens defending them. UFO crash sites are determined by a few factors, if a UFO is shot down at a high altitude, the chance for a UFO being destroyed outright is higher. The lower the altitude, the higher the chance of a crash site. In the off chance that a UFO is shot down from high orbit, there is a higher chance for valuable equipment to be destroyed when your troops arrive.
UFO Landing Site
Some UFO missions will involve a landing. Whether or not this will be the case can often be determined by looking at the UFO's altitude (NOE altitude often means it will land). If you allow the UFO to land it will either generate a terror mission, an abduction, or simply a landing site. It may actually be in your interests to let low-flying UFOs land, as (a) it will save your interceptor craft some damage, and (b) it will net you a lot more salvage, including intact computers and generators. On the other hand, the landing UFO might generate an abduction instead, in which case you lose the salvage you'd get from a crash site. Successfully assaulting a landed UFO will also stop the alien mission from being completed. Be warned some UFOs are crewed by elite crews; these will have a large number of strong aliens defending them.
Note that in either Crashes or Landings, the CO pod of aliens will now rarely, if ever, be on the bridge (and for the Small Scout, it might be 'slightly outside'). This is so you won't know exactly where this pod is, and thus won't be able to prepare a blitzkreig to take it out.
Terror Site
Similar to vanilla terror missions. You are required to eliminate all hostiles and save as many civilians as you can. Long War is very unforgiving of allowing civilians to die, and you will need to save almost all of the civilians to avoid panic rising in that country and continent. Terror missions are generated by UFOs, so you can prevent a terror mission by shooting down the incoming UFO before it can create the terror site. Like vanilla, failing or ignoring a terror mission will cause the targeted country to leave the project immediately.
XCOM Base Defence
This mission type makes a return. When the aliens have high resources AND consider you a high threat they will come for your base. Your base is assaulted by a UFO, which you can see coming (typically a NOE altitude Assault Carrier in your home country making a bee-line for your base) and can shoot down, but it's extremely difficult. Like vanilla, you'll get the top 6 soldiers on your roster in this mission. Fatigued soldiers will still be fielded, but any wounded, psi testing, etc. soldiers will not. Try to spot the assault coming and quickly equip those soldiers.
The format of the mission is similar to vanilla, the aliens will drop in to the command center, followed by flyers in the back and drops in to the mech bay and two waves in the forward access tunnels. Expect this mission to be very difficult (though exact forces deployed are subject to RNG, so it may be nice to you).
Failing this mission does not mean the end of XCOM, however it is extremely damaging. Besides losing your top soldiers in combat, the aliens will ransack your base, killing engineers and scientists and destroying cash, meld and other currency before regular military arrive and bail you out. This mission can happen multiple times in a game. If you succeed, any surviving Blueshirts will join your roster.
Council Missions
Council missions have also been modified, mostly to the tune of larger numbers of enemies, both seeded and airdropped. For example, the Site Recon mission has number of free-roaming Chryssalids. Keep an eye on your ammo. However, the mission objectives have not changed from vanilla XCOM Enemy Unknown/Within.
EXALT
Covert Data Recovery
These missions are similar to their vanilla equivalent. You field a full squad and defend an encoder and transmitter. Comm arrays are available for your covert operative to hack. This mission will give a cash reward, and a bonus if the encoder is protected as well.
Covert Extraction
In this mission type you are limited to only 4 soldiers and your covert operative. As such, you want to avoid getting in to a pitched battle with EXALT, so if you can, try to get your covert operative to the arrays, hack them and get out fast. Cash reward on completion.
Exalt Base Assault
This mission is considerably tougher than it is in vanilla. The EXALT base is crawling with randomly generated elite EXALT squads. In addition you may find some elite aliens here as well.
Long War makes a tweak to the hologlobe UI so that if a mission is outstanding, time acceleration will stop when interesting things like a soldier recovering from fatigue happens. This means you may want to avoid the final "discover" step on the EXALT base until you're ready to assault it to avoid this behaviour triggering constantly even though you don't want it.
Essential Missions
Alien Base Assault
Like in vanilla, story progression is nearly the same. But in the Long War, you will immediately lose 1 country on the first month, as the base is auto-generated at this time. Progress as normal to be able to develop the Skeleton Key, and then place a satellite over that country (or any others you lose along the way: they will also spawn bases) to locate it. Expect 4-5 large-numbered pods to appear in the first room alone. With that in mind, you may want to either take your first Assault as soon as possible, as to face weaker aliens, and/or after buying both Squad upgrades and the Super Skyranger Foundry project for the added soldiers and firepower. That way, even if you do lose more countries, but don't want to risk soldiers attacking another Base, at least you can still progress with the storyline.
Like with UFOs, the commander will not necessarily be in the last room with the Hyperwave Beacon, so this isn't necessarily the best place to capture one like it is in vanilla.
Long War makes a tweak to the hologlobe UI so that if a mission is outstanding, time acceleration will stop when interesting things like a soldier recovering from fatigue happens. This means you may want to delay putting a satellite over an alien country until you're ready to assault it to avoid this behaviour triggering constantly even though you don't want it.
Overseer Crash Site
Also like vanilla, mostly the same, but also with the same difference: you may encounter mutliple Overseer UFOs throughout a campaign. Possibly the only UFO where the CO pod is in the usual spot.
Temple Ship Assault
It's been a lengthy journey, but the end of the Long War is in sight!
The Temple Ship is near-identical to in vanilla: same enemy composition and positions as Enemy Within/Unknown, albeit with vastly increased health, stats, and gene mods (aand size, for that extra player intimidation factor). If you've survived EXALT and an Alien Base or two, you should be fine. At the end of the brutal road, in the Ethereal Cathedral awaits the Uber Ethereal, Lord of the alien collective. On the easiest difficulty alone, he has 80 HP, and about 300 Will.
Good luck, Commander.