Storyline Missions (XCOM2)
The tutorial mission is entirely scripted, designed to introduce you to various concepts. There is no way to change the events, and you will always finish the mission with two casualties, and one soldier (Jane Kelly) on your roster at Squaddie rank. It's recommended to play through your first time with it on, since it also contains plot exposition that you otherwise miss. Do note that tutorial makes The Untouchables achievement unattainable.
The Commander of XCOM (you) had been captured a few weeks into the campaign of the war in 2015: having been in stasis for 20 years, the tutorial will guide you through with Bradford himself pulling you out of an ADVENT facility. As you leave the area, an electrical surge burns out the remaining equipment, and a Codex appears and notes your disappearance.
The Commander is taken to the Avenger, where Dr Tygan performs an operation to remove an implant from your brain to restore you to health. You are then encouraged to browse the history database and then are introduced to Dr Tygan, the chief scientist, and Lily Shen, chief engineer and daughter of Raymond Shen.
You will quickly be launched in to a second mission to obtain a power core for the Avenger to make it flight ready. This mission is not scripted.
If playing with tutorial off, the game will instead start in a 4-person mission to destroy an ADVENT monument, to provide a distraction from the recovery of the Commander. The Avenger is already fully functional and the mission to recover the power core doesn't occur.
You will have a research topic available to research the implant removed from your brain, then an autopsy to take a similar implant from an ADVENT Officer. Researching this will reveal that all of the ADVENT troops are linked together by these implants, and that accessing a live officer's implant could allow XCOM to pull information from the aliens' psychic network. You then need to construct a Proving Ground and research the Skulljack. This will give an objective to Skulljack an ADVENT officer in the field.
Meanwhile you will be contacted by the former XCOM Council Spokesman, who will inform you of a "Blacksite" that seems to be a focus of alien activity. You need to research Resistance Comms to contact other regions and contact the region containing the Blacksite to gain access to the mission, after which you can launch it at any time.
This is a retrieval and extraction mission. Your squad is inserted some distance from the Blacksite in concealment. Upon approaching the Blacksite you will see that it's a processing facility turning humans into some sort of liquid, and you must recover a vial of this substance and extract it to the Avenger. This mission has more enemies than missions so far, and is likely to be your first encounter with ADVENT MECs, and ADVENT Turrets.
Completion of this mission allows the research of the Blacksite vial. This requires building a Shadow Chamber facility first, and completing the analysis unlocks the Forge mission.
Skulljacking an Officer
Upon skulljacking an officer, a Codex will teleport in. A Codex is likely much stronger than anything you've encountered so far (depending on how long you put off Skulljacking), so you'll want to wait until things are quiet before doing the Skulljack. Killing the Codex will reward you with a Codex Brain to research. Note that you will recover the Codex Brain after the killing the Codex even if you extract from the mission.
Analyzing the Codex Brain requires the Shadow Chamber facility. Completing this analysis unlocks the Psi Gate mission, and Skulljacking a Codex in the field.
Analysis of the Blacksite Vial in the Shadow Chamber will reveal the presence of another alien facility. Infiltrating this facility, you discover an environment suit similar to the one you were imprisoned in, and you are tasked with recovering the suit and occupant and extracting with it. This mission is guaranteed to contain a Sectopod.
Researching the Codex Brain unlocks this mission to investigate the point of origin of the Codex. You approach in infiltration and find a Psionic Gateway, guarded by a large number of Chryssalids and other enemies. In addition, when you get close a Gatekeeper will come out of the gateway to defend it. You must defeat all enemies to secure the site.
This will allow you to install the Psi Gate in to the Shadow Chamber. Researching the Psi Gate shows it to be a gateway to the aliens' base of operations, but efforts to send a probe through fail due to needing an organic key of some sort.
Skulljacking a Codex
After completing research on the Codex Brain, Tygan will ask you to Skulljack a live Codex in the field to allow further access to the aliens' psionic network. Skulljacking a Codex spawns an Avatar enemy, at reduced health. Killing the Avatar allows its autopsy.
ADVENT Network Tower
Analysing the Avatar corpse requires all other storyline research to be complete. This will trigger ADVENT to accelerate their plans for humanity and start processing all humans in to genetic material in the gene therapy clinics. The Spokesman will contact you with a plan to assault the ADVENT central network tower to capture it and broadcast the truth to the population, and also to distract ADVENT from an XCOM assault through the Psi Gate. The assault on the ADVENT network tower will then be unlocked, though you don't have to accept it yet if you don't want to.
Launching the assault on the ADVENT network tower locks you in to the end-game sequence, so be sure you're ready to finish the game before doing so. The ADVENT tower assault is a small penultimate mission, where a small squad of infiltrators must attack the tower. You can spend any remaining Intel you have on bonuses to make this mission easier. You must fight through the tower's defenders (a relatively small number of high powered enemies) to hack the network tower's control panel and extract.
Alien Fortress - "Waterworld"
After the network tower mission, you will immediately launch in to the final mission of the game. You can field wounded soldiers in this mission, including any wounded in the network tower assault.
XCOM launches an assault through the Psi Gate to the aliens' base, accompanied by an Avatar controlled by you, the Commander, personally. Losing your Avatar in this mission immediately loses the game. As you move through the level, Central, Shen, and Tygan will keep you updated on the situation here and on the revolution across the Earth, while the Speaker, the female-sounding 'Angelis Ethereal', and a more aggressive male-sounding one attempt to persuade and goad you. After fighting through a variety of enemies, you will reach the final room, full of psionic gates.
After a cutscene, an alien Avatar will be on a raised platform up high in the middle of the room-- and can be flanked from the left path, being spotted by a soldier in concealment and a Sharpshooter using Squadsight from the full cover pillar near the statuary. It will move to engage you when spotted/wounded (and the game may glitch if this first one is Executed via a Repeater before waking the pod up). After a turn or two, two more will spawn in from the other portals, accompanied by alien pods of varying composition and threat level. Killing all three Avatars wins the game, so keeping away from the other aliens to focus on the Avatar may work as a last stand, even if means continuously falling back through the level to keep ahead of the aliens.
With the last enemy Avatar destroyed, the psionic network holding the Gates active begins to destabilize, with the alien base starting to self-destruct from the strain. The Gate in front of you collapses, but you manage to wedge it open with Psionic power and send your troops back through. With no other options left, the Ethereal bodies glow from their 'coffins' strewn about the room, and attempt to overwrite you from the Avatar body. Fortunately, they have greatly underestimated you, and you are able to hold your own against the full squad of Ethereals, singlehandedly. Blasting back the wraith-like entities they have become, you destroy their fortress and also manage to get your own consciousness back, waking up in your real body - with an otherworldly sound not unlike when Asaru contacted Faulke, Wier, and Weaver...
The true leaders of ADVENT destroyed, their atrocities exposed and their psionic network in ruins, ADVENT forces crumble before the now exponentially more empowered and numbered Resistance. The people have awoken and are striking down ADVENT, taking back their world. Those with the War of the Chosen DLC will also be treated to several other cutscenes: the Reapers rising up to face ADVENT in combat, an ADVENT squad being admitted into the Skirmishers, and the Templars predicting that the war is not over just yet.
Mission complete, Commander!
The ocean had rushed in, the immense pressure destroying the alien fortress, leaving debris and alien bodies scattered all about the seabed. The last bit of light leaves as the Ethereal 'coffins' flicker and go out... save for from one fissure in the rock, where Psionic energy seems to stream out of the gap in the Earth. Is this truly the end of the Ethereal invasion? Or is this a sign of a new rising Terror From The Deep? Only time will tell...