Story Thread 1
The earth is heavily contaminated with Kojima Particles after the Linx War (AC4). The major companies rebuilt themselves and formed the League of Ruling Companies, creating the Collared Organisation to control the remaining Linxes, so they wouldn't begin to act independently and start another war. An uneasy peace is maintained. The companies still fight among themselves, and they create Arms Forts to increase their war-fighting capabilities. You are part of these small skirmishes as the companies continue to jostle for power behind the unified façade of the League.
The companies launch unmanned Assault Cell satellites (orbital cannons) into low Earth orbit to prevent any one breakaway faction/company from going into space (because they don't trust one another), thus effectively preventing the human race from leaving Earth. In this way the League maintains control of the planet.
Most of the world's population now lives in Cradles, huge jets that cruise in the stratosphere, just below the orbital guns. Each one holds 20 million people in extremely cramped and overcrowded conditions. They are powered and controlled remotely from the ground by Carpals, the most important one being the Arteria Carpals, a seawater fusion reactor that is controlled by Rosenthal. Power is transmitted to the Cradles by machines that look like large cannons. In the event that the Cradles lose all power from the ground transmitters, they are designed to be able to glide on reserve power back to the Earth for an emergency landing.
When you begin the game, you fight various battles for the individual companies, but occasionally the League will give you a mission to wipe out small bands of rebels. One of these rebel groups is Line Ark, a small independent protectorate comprising the remnants of the Aspina and Anatolia colonies. The mysterious White Glint is the sole AC of Line Ark, and the pilot is the main character from AC4. Fiona Jardenfeldt is his operator. The first mission you are assigned requires you to attack Line Ark, and you destroy a few of Line Ark's MTs and Normals. A short time afterward, Line Ark forces hijack Cradle 21, and you are sent by the League to recapture it.
Eventually, after various contracts for the companies, you are asked to go with the top Collared ace Otsdarva (piloting Stasis) to destroy White Glint. During this battle, Otsdarva encounters engine trouble and his Next falls into the sea. You finish off White Glint, and Line Ark is no longer a threat to the League.
<In an alternate story branch, you are hired by Line Ark to protect the Megalis, their sole power installation, from an attack by Omer. In this branch, you will later fight alongside White Glint against Otsdarva and Cube. White Glint is disabled during this battle, and Line Ark ceases to be a viable military force.>
You continue to fight various battles for the companies, until the Arteria Carpals comes under attack from a previously unknown group of rebels, the Orca Brigade. You are sent with Noblesse Oblige to aid in the defense of Arteria. <THIS IS THE CRUCIAL POINT WHERE THE STORY BRANCHES>.
Orca is a large, well-equipped rebel force led by the enigmatic Maximillian Thermidor, and they aim to bring the Cradles to the ground and destroy the Assault Cells so the population can expand into space, and the League's iron grip over the Earth can be disrupted.
They seize control of the Ehrenburg Satellite Cannon installation and GA's headquarters (Big Box), and eventually retake Arteria. You have to defeat Orca at all 3 sites and destroy the Orca Arms Forts to finish the first story thread, where you preserve the existing hegemony and allow the League to remain in power. The first thread ends with the Answerer firing its main cannon as all the Orca rebels are crushed, and the population stays in the Cradles, living as refugees in miserable conditions high above the earth. Boo Hoo.
Story Thread 2
After the Battle at Line Ark (White Glint battle), you receive a transmission from Orca. It is Thermidor, and he convinces you to switch sides and attack the Ulna Carpals, a wind power installation controlled by GA. Upon completion of this mission, you become an operative of the Orca Brigade. The Arteria Carpals are now the sole source of power for the Cradles. You are sent on a solo mission to capture Arteria, where you defeat Noblesse Oblige and another Collared AC. Orca simultaneously take the Big Box and the Ehrenburg guns. You repulse 2 counterattacks by the League to destroy the Ehrenburg and retake the Arteria Cranium, which controls the Cradles. You also destroy the Answerer, the League's primary Arms Fort that uses a new type of Kojima technology.
Thread 2 ends with the Cradles being brought down to Earth to liberate the population, and the firing of the Ehrenburgs to destroy all the Assault Cells orbiting the globe. Mankind ascends to the stars, escaping the decaying and polluted Earth.
Story Thread 3
After switching sides to work for Orca, a hardline extremist member of the Brigade approaches you:
"Greetings, Collared Man. My name is Old King. I'm planning an attack on the Cradles.....are you with me? The Orca Brigade's revolution isn't enough to change things, and they will all die trying, wouldn't you say? I say we take down as many Cradles as we can. If we're all going to die, we're not going to go quietly."
You carry out Old King's orders. You shoot down Cradle 3 and the 4 Cradles flying alongside it. 100 million people die by your hand.
Not long afterward, you receive a transmission from Interior Union, one of the companies that comprise the League. They want you to proceed to the Arteria Carpals to secure the facility against an attack by Orca. It's a trap, they set you up. You go with Old King to the Carpals for the final confrontation. The League sends the top 4 Collared Linx to fight you: Roadie (GA), Wynne D. Fanchon (GA), Lilium Wolcott (BFF), and Otsdarva/Thermidor, who is actually a double agent for the League. He faked his own death during the battle with White Glint, emerging as Thermidor to lead Orca, whose members had been waiting for him. Your operator, Kasumi Sumika from AC4, who abandoned you after you massacred 100 million people, also appears in her AC to fight you.
During this battle, Old King is killed, but you manage to wipe out all 5 enemy ACs, becoming THE LAST LINX. YOU ARE A BADASS!!