http://tvtropes.org/pmwiki/pmwiki.php/Timeline/MarvelAvengersAlliance

With a game which is Merchandise-Driven meets a format that's pay to win, plus Continuity Snarl and the vast lore of the marvel universe, the timeline of Avengers Alliance is an extremely long, extensive, and even lost timeline due to the nature of the Special Operations Missions. And, of course, spoilers.

Help with the timeline please, as we're bound to miss a part or two in the process.

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Before The Pulse

In the ancient past, Odin, king of Asgard, overthrows his brother Cul, defeats the Dark Elves and stops the attacks of Surtur.

HYDRA is formed under the Red Skull. However, he is killed during World War 2 by Captain America, who is subsequently frozen in ice for decades.

After getting dosed by cosmic rays, Reed Richards, Susan Storm, Johnny Storm and Ben Grimm are transformed into the Fantastic 4.

Dr. Doom makes himself King of Latveria.

Peter Parker is bitten by a radioactive spider, becoming the Spider-Man.

Magneto earns the ire of SHIELD due to his mutant supremacy issues, making him the #2 most wanted man on SHIELD's criminal watch. Meanwhile, HYDRA survives into the modern era under new leaders, such as Viper, Baron Zemo II, Baron Wolfgang von Strucker, Arnim Zola and other various factions. Baron Zemo spends some time consorting with the infamous crime leader Count Nefaria, father of Madame Masque. After learning for a time, he returns to gain power in HYDRA again.

Iron Man begins his direct involvement with SHIELD and is promoted to primary consultant alongside Nicholas Fury and Maria Hill.

Wilson Fisk takes control of various criminal factions, eventually coming to be called The Kingpin of crime. Hammerhead, Madame Masque and The Hood are various other criminal leaders who rise to prominence in this time.

The Advanced Idea Mechanics (AIM) is formed, with their leader MODOK seeking control of Earth through a technocracy. RAID splits off from AIM as another form of technological control.

The Guardians of the Galaxy are formed with Star-Lord, Gamora, Rocket Raccoon, Groot and Drax as members. Other members such as Quasar, Adam Warlock, Cosmo and Mantis join up as well.

The Avengers are slowly formed up from superheroes across the world, though, as times grow quieter, not all of them are held in active duty.

The Runaways...well, run away from their supervillain parents.

A nameless S.H.I.E.L.D. Agent is prepped for active duty by Maria Hill.

The Pulse: Opening Actions

As a phenomenon known as the Pulse sweeps across the planet, the S.H.I.E.L.D. Agent is mobilized with Iron Man to aid Black Widow in New York against AIM forces.

After being assisted by Iron Man and the Agent, Black Widow joins the Alliance. They subsequently team up with Captain America to defeat a Hydra Power Armor robot.

Reed Richards researches a meteorite that materialized in the wake of the Pulse. The meteorite is identified as Isotope-8 and is used by the Agent to augment abilities.

With the Pulse and criminal organizations leaping into action more vigorously, Nick Fury sounds a red alert, reactivating all Avengers to deal with this new threat to civilization.

In the Meat Packing District, the Agent's team aids Hawkeye in stopping Hydra operative Viper. As it turns out, Viper was running distraction for someone else so that they could make off with an unknown object.

The Hydra agent who escaped custody is tracked to Empire State University and apprehended by Hawkeye. Elsewhere, the Agent assists Iron Man in defeating RAID and AIM forces led by Whiplash.

The Agent is sent to assist Captain America against Hydra soldiers marshalled by Baron Zemo. At the same time, a large energy reading emanates from the Financial District.

The team fights AIM.

Thor leads an attack on Frost Giants being lead by Loki, who has some kind of knowledge of the pulse but won't tell about it.

Hulk and several other large sentient creatures fight around a large machine which helps manipulate them to do battle.

Trouble In Hell's Kitchen

Hell's Kitchen begins breaking out into gang warfare, as various lower criminals such as the Hand, the Maggia and RAID start getting active as well.

The Crimson Dynamo leads a team of Doom's robots against Avengers Mansion.

Doom Rising

Dr. Doom enters the field for the first time.

U-Foes Running Amok

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Loki's Stone Days

Loki threatens to turn New York to stone, bringing on the Wrecking Crew to run interference.

A Mysterious Shipment

Madame Masque takes on a mysterious shipment, passing it on to other groups, such as the Hand.

Lead by the Juggernaut, mutants and prisoners lead a riot at the Raft.

Demons And MIA

Different demonic groups begin appearing around New York. One such group is lead by Jack O'Lantern.

Going to the Latverian Embassy on Doom's request, Nick Fury and Maria Hill go missing, reported as MIA.

Wanting to send a message to Doom for potentially hiding Nick and Maria, Tony orders a hit on the four U-Foes who had been working under Doom.

The Hunt For Nick And Maria

The Avengers stop a raid in Bellevue, Washington.

Capturing the Omega Sentinel, Tony and the other geniuses manage to deprogram her to remember her past life as an Indian cop. She then joins the Avengers.

The Syndicate Revealed

Picking up a distress call from around the Raft, the Avengers intervene, sending Ben Grimm down to pick up Nick and Maria. The two of them reveal that they've discovered a connection between different villains, with different villains joining up to exploit Iso-8 and rule the world.

The heroes witness the Hood dying and resurrecting himself.

Doom formally reveals the Syndicate, with HYDRA and the Brotherhood of Evil Mutants as his wings.

Using resurrection magic, the Hand does HYDRA's dirty work and resurrects Red Skull.

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Mutant Island

"Magneto" declares Manhattan a new mutant kingdom and begins to work to create a new haven for mutants.

Turning on them, HYDRA begins attacking Brotherhood supporters as a way to consolidate their own power.

Speaking to SHIELD, Magneto asks for their help, but as an equal. Then, when "Magneto" tries to release spores that would turn all of New York into mutants, Magneto steps out once again, revealing that he was against The Syndicate and that the "Magneto" leading the plans at this time was Mystique. Stopping the machine, Magneto formally joins the Avengers, promising to help in their battles, so long as they can help keep mutants safe.



Battle Royale

All hell breaks loose in New York as various criminal factions begin fighting for dominance and the privilege of being part of the Syndicate.

Loki leads his faction of magical forces to cause chaos in the world. They're shut down, from the Wrecking Crew to Loki himself.

Hydra leads different factions in an attack on New York, with Zemo and Viper leading different factions in the process. They are captured, and sent to the Raft.

The Hood leads the Maggia and other lowline gangs in an audition for Dr. Doom, with Dormammu revealing himself again at this time as well.

AIM lead by MODOK also leads a supervillain faction in an attempt to gain access to the Syndicate, but they too are driven off.

En route to the Raft, Zemo and Viper are freed as the leaders of various factions attack around NY, with Red Skull revealing himself for the battle as well. Magneto battles Red Skull.

Dr. Doom unleashes a swarm of Doombots and Servo-Guards, stating that using a modified version of the machine used on Hulk in the opening acts of the Pulse was responsible for this rash of supervillain attacks in a way to gain power for himself. He tells of how the Pulse is an omen of greater things, but he's driven back into his embassy, his plans foiled for now.

Ultron Unleashed

Realizing the Pulse created a rogue signal around the globe, the Avengers call on Dr. Henry Pym to harness the intelligence into a new body to be controlled. In the process, the intelligence is almost stolen by HYDRA. Worse, Kang the Conqueror arrives in the past, saying that Pym's actions will lead to the destruction of Earth. Still, Pym persists, placing the intelligence in a body and giving it a designation: Ultron. Unfortunately, Kang's prophecy rang true, and Ultron turns on Hank and the Avengers, seeking the annihilation of humanity.

Escaping into the Internet, Ultron then builds multiple robot duplicates of itself to destroy the world with, as well as a robot lieutenant: the Vision. However, in the course of battle, the Avengers capture Vision, help reprogram him, and turn him against Ultron, ending his killing spree for now.



Great Britain's Opening Act

Agent Phil Coulson joins the operating staff as tactical adviser to the team.

He then leads the Avengers abroad to fight alongside Excalibur: Britain's version of the Avengers. Partnering with new heroes like Union Jack, Captain Britain, Psylocke and Black Knight, they join a fight over the Philosopher's Stone. Dr. Octopus then begins his own work, saying he needs to find a solution to the Incursions popping up from other universes.



Danger Among The Mutants

With Magneto defecting to SHIELD, Mystique takes control of the Brotherhood of Evil Mutants, leading them on new raids in her quest for power to survive.

Discovering The Circle Of 8

All the mysterious writings, clues and signs found before now are revealed to be the work of a real cult: the Circle of 8. Their purpose is to sacrifice others to bring about the fall of 8 hammers so as to bring forth the Serpent Cul and cleanse the world.

Gang Wars

With the shakeups thanks to the Syndicate wars, supervillains begin fighting for control of the various criminal factions. Not helping at all is that HYDRA begins fracturing under its own weight as Zemo and Viper fight for the honor to be Red Skull's #1.

The Maggia begins to splinter, with new villains such as The Grim Reaper trying to claim the organization for themselves.

Inhumans And Thanos

Thanos the Mad Titan comes to Earth for the first time in years.

To fight against him, the Avengers recruit Black Bolt, King of the Inhumans. In time, the rest of the royal court joins up from queen medusa to all the royal councilors.



The Savage War

Warfare breaks out in the Savage Land between people in expedition to the lands and local powers, such as Sauron.

Wakanda Under Siege

The Nation of Wakanda comes under attack, as HYDRA allies with the White Gorilla armies of Man-Ape to gain resources for themselves.

Fear Itself

While investigating the Circle of 8, hammmers begin falling from the sky, signaling the beginning of the return of Cul and the Serpent and the beginning of Ragnarok.

Killing D- and Z-list villains, the Circle of 8 begins to call down hammers for various people to take on a new identity. The first is She-Hulk. Second is Sin, Red Skull's daughter, who becomes Skadi. She drops during a demonic invasion, and is mistaken for a demon at first, but establishes herself as Cul Borson's hand on Earth. Then comes Luke Cage. This is followed by Spiderwoman.



Defenders Of Midgard

Surtur the Demon of Muspelheim leads an invasion of Earth with other powers like the Dark Elves and the Frost Giants (lead by Malekith and Ymir respectively). They intend to grab up power on Earth before the Worthy take over.

Thor goes to Asgard to ask for help from his father with Earth's dilemma. Due to his own relative weakness, Odin refuses.

Shifting Powers

Trying to gain control of the Mindless Ones, Baron Mordo is killed by Dormammu. In response, the demons rise up in outrage, plunging New York into the middle of a demon civil war.



The Runaways Undercover

With the Avengers missing, Maria Hill deputizes the Runaways to investigate the Kingpin as moles. Under The Kingpin, the Runaways quell various gang wars, and then move on to fight ULTIMATUM and their "leader" Flag Smasher in their attack on the UN.

Kingpin, however, knew they were moles all along and instead advises SHIELD to "follow the money" to try and find greater opponents than just himself.

The Age Of Ultron

Using ULTIMATUM and HYDRA as patsies, and turning Scarlet Witch and Quicksilver against the Avengers, Ultron reaches Wakanda and creates for himself a new Vibranium body with which to fight with.

However, he's still driven off all the same.

Spider Universe

A new foe begins terrorizing New York, as the Sinister Six reform to capture Spider-Man for Doctor Octopus. However, a further complication arises when Spider-Men begin appearing from other universes as well.

With new Spider-Men such as the Superior and Ultimate Spider-Man working together, the Sinister Six are defeated, as well as their true backer: the Green Goblin. However, with the multiverses still in trouble, two other Spider-Men (and woman) decide to stick around and help the Avengers.

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The Pym Thefts

Hank Pym's labs are raided, with his LM Ds of the Avengers being stolen and hijacked by a man who also steals the Yellowjacket armor. Also at this time, Scott Lang, a small time thief, steals one of Pym's Ant-Man suits. Working together, and chasing the thieves around New York, the Avengers put a lid on AIM's goals to take control of Pym's technology (they provide Whiplash to help with the thefts, and even MODOK attacks at one point). Helping to defeat Yellowjacket, Scott Lang is recruited as the newest Avenger.



The Quest To Stop Cul

Searching for another Worthy touchdown, the Avengers happen upon an Incursion site that appears and disappears. Fighting scientific and tech minds such as Zola and Mysterio, they also find more dead villains. They happen upon a new Incursion, when it disappears as The Mandarin appears on the battlefield for the first time, declaring that he destroyed that universe for the good of theirs, and that Iron Man understands this as well. After Psylocke and the Agent chase the Mandarin away, they happen upon a new Worthy: the Breaker of Oceans, who just happens to be Mockingbird, explaining why she never returned calls after finding another Circle of 8 corpse.



The Sorceresses Strike

Morgan le Fay, Hela and Umar plot to conquer the Dark Dimension and London, planning to use Dracula as a patsy for their plans.

However, it's at this time that Dr. Strange discovers Baron Mordo was not killed, but merely captured for the purpose of draining his magic for their rituals. Entering the Dark Dimension, Strange rescues Mordo, and with his help, leads a series of attacks on all 3 forces, foiling their plans. With their end, Baron Mordo joins on as a new Avenger, his anger at the forces of evil for torturing him overruling his hatred of Dr. Strange.

Also at this time, a new Avenger joins up: Spitfire, a vampiric member of Excalibur, called in for this mission.

The Gang Shakeup

Boomerang attacks the Shocker, telling him to tell his boss the Kingpin that the Owl sends his greetings. Outraged, and seeing factions of the Maggia siding with Owl, Kingpin takes to the street in order to stamp out the challengers. Meanwhile, the Beetle begins wrecking havoc, and Hammerhead does as well. To combat this new New York gang war, the Avengers activate new heroes Misty Knight and Luke Cage's wife Jessica Jones. Both pledge to clean up the war.

In the field, a hero discovers a purple vial being carried by one of Kingpin's men, which Hank Pym identifies as pheromone suppressors. In turn, Jessica recognizes that these are vials used in dealing with a villain from her past: Zebediah Killgrave, also called the Purple Man. In the past, Purple Man caused Jessica to see and do "horrific" things, until the Phoenix managed to put up mental shields so she couldn't be controlled by him anymore. She figures that he's manipulating this gang war between the Owl and Kingpin for his own purposes. Meanwhile, in a battle with Hydro-Man, who's also searching for Purple Man, Zebediah takes control of Hydro-Man after the battle, warning Jessica that even though she's now immune, other people aren't, and their engagement is just beginning.

Because of the Owl and Purple Man's pressures, Kingpin is attacked by SHIELD for the first time in the conflict. Though he escapes, SHIELD promises to bring an end to his reign before long.

The Leader Moves In

Betty Ross, Red Hulk's daughter and Bruce Banner's wife, is kidnapped. It turns out the Leader, longtime villain of the Hulk is behind it, who's employing Absorbing Man, Abomination and the Winter Soldier in his care to succeed. However, during the course of the search, the team reaches Betty before she can be taken away from the area, revealing that the Leader did the same procedure on her as her father, turning her into Red She-Hulk. Fighting off Abomination with the team, Betty seems to remain in control of her faculties, though SHIELD still takes her in for psychiatric evaluation. Meanwhile, the team begins a man-hunt for the Leader.

Fighting through Abomination, suddenly Skirn (She-Hulk as a Worthy) comes to fight too, seeing potential in making Betty a Worthy. Thankfully, they drive her off. Meanwhile, Red Hulk manages to find the Leader and his AIM forces. He attacks him, seeking to burn him using his powers, but instead the Leader absorbs the red energy, becoming Red Leader. He manages to escape but, as a side effect, the Leader's control over Winter Soldier is broken. As a result, Bucky reaches out to the Avengers, telling them about the Leader's TRUE plan.

Bucky reveals the Leader's plan to detonate a gamma bomb on San Francisco to create a gamma army. Though he intended Red She-Hulk to be its leader, he decides to proceed nonetheless. While keeping an eye on Bucky for any treachery, Red She-Hulk reaches the Leader, She reveals that she was actually a bit uncomfortable with the transformation, but she then beats the red energy out of the Leader, capturing him. With his defeat, Abomination, Leader and Absorbing Man (another minion beaten during the kidnapping) are sent to the Raft. And while Red Hulk is sad that his daughter had the Hulk curse put on too, Betty is determined to fight the good fight regardless of what her father wants. Hulk, meanwhile, goes off to sulk at losing his wife to the gamma too.



Incursion Madness

Wanting to experiment with a new device that would help patch Incursions, Black Panther and Nick Fury experiment with a new device in Wakanda. Unfortunately, the land is attacked again by the White Gorillas, who this time ally with AIM and MODOK, who are also looking to deal with Incursions. While they're repulsed, the device malfunctions, trapping Nick Fury in another universe, forcing the other 3 leaders to consider him MIA while Panther tries to find him again.

At this time, as well, a team of Sentinels the Fixer was messing with go rogue, leading Quake to be activated to deal with them. Also during this time, the team discovers where Damian Hellstorm disappeared to: he was the next Worthy as the Breaker of Souls. It turns out that Bastion was behind the rogue programmings, though Ultron was also using them for his own ends.

The Avengers then get a tipoff that the infamous Count Nefaria is starting to get involved too. He seeks to find K'un Lun, the place where Iron Fist got his training from, as a place to survive the Incursion crisis. He even united factions of the Maggia and Hand to try and do so. Sunfire drives him off from his home base of Madripoor. Also during this time, Cyclops takes up protecting the government of Madripoor from this crisis. But before leaving, Moon Knight brings intel that the Mandarin is in the area, leading another strike on him, and capturing the Living Pharaoh in the process. But before escaping again, the Mandarin says that in their attacks, they neglected to keep their own home secure. Upon returning to New York, they find Avengers Tower destroyed. Outraged, Tony wants to lead an immediate manhunt for the Mandarin, but Thane then comes in asking for help as the captains of Thanos are also waging war on Earth, planning to destroy it to stop the Incursions. They fight them off. Also at this time, Mr. Fantastic and Magneto stop Ronin from disrupting their efforts to use magnetism as an alternative way to deal with Incursions.



Masters Of Evil: Headhunting

The younger heroes (Kate Bishop, the Runaways, Kamala Khan, Nova, Cammi, Squirrel Girl, Miles Morales, Spider Gwen, Amazing Spider Woman, and Spider Girl) are somehow transported to the Savage Land to be "tested", and show their commitment to do what needs to be done.

The New Civil War

With the aid of a "profiler", the Inhumans invade Latveria, upsetting SHIELD's alliance with Dr. Doom. The Avengers are split over this action, as it was an unprovoked attack, and done with "future knowledge" rather than hard evidence. Iron Man favors sticking to traditional methods of action as the future is unpredictable. Ms. Marvel (or Captain Marvel depending on what you've unlocked), however, thinks that with the dangers they've faced all over, especially the Serpent crisis, they need a leg up through this predictive action. The Agent sides with one side or another, but both choices lead to disaster. Siding with the pro predictive side leads to raids on Vibranium from Wakanda, and engagement across the globe with help from the hero Blue Marvel, but victory only leads to the High Evolutionary detonating a bomb which ends up mutating the Earth. Siding with the anti predictive side leads to fights across the world, and recruiting help from Ultron while battling Inhumans as well as the pro side. Edged on by a version of Thor from "the future" (A future where Jane Foster took up the mantle), however, by the end of it, Ultron betrays them, and causes Nuclear Armageddon. Kang the Conqueror (who by this time has become an ally to save the future) takes the Agent back from both futures, and unites Blue Marvel and Jane Foster's Thor to convince the leaders to stop their paths towards destruction. Though it requires battles with the leaders to get them to change their mind, eventually the Avengers reunite again. To that end, they end up engaging with the true threats to the planet: the High Evolutionary and Maximus the Mad. Maximus in particular was the one who started the whole mess anyway as the profiler's interpreter who twisted his words, and the Avengers drive him off again.

After this, Dr. Doom declares his intentions to leave the alliance to save the world his way due to what he learned about the profiler, but Jane Foster's Thor and Blue Marvel stay on as new recruits.

The Black Vortex Crisis

The guardian Mantis comes to the main Guardians of the Galaxy, asking for help protecting an artifact she stole from Star-Lord's father: J'son. Called the Black Vortex, it's said that it can grant power and desire to those who stare into it. She goes to the Guardians to help keep it from J'son, who hid it on Earth, keeping it a secret from all non-Guardian heroes. However, Mantis's partner Moondragon is taken over by the power of the Black Vortex, and she leads a strike against the Guardians to retrieve it with Nebula's help. While the Guardians beat them off, the Black Vortex goes missing after the battle.

Going for help to the Avengers, it turns out the Hellfire Club, Ronan and Star-Lord's father all have troops in the fray, being empowered by the Black Vortex. Leading the X-Men due to the Hellfire Club's involvement, Kitty Pryde takes the lead alongside Star-Lord hunting the Black Vortex. In the process, they fight Mystique and Bastion, who was using the Vortex to empower the club for the future. Ronan the Accuser then looks into the Vortex, empowering himself and giving the corrupted Moondragon space to flee. Though they drive him off, Mantis begins wondering if she should submit to the Vortex for the power to achieve victory.

Chasing J'son's Spartans to Madripoor, J'son makes an announcement to use the Vortex's power on his legions to destroy and thus end the Incursion crisis. Battling across Madripoor, Star-Lord and Kitty Pryde join the Agent in a final battle with Ronan, Moondragon and the Black Vortex itself. After a prolonged battle, the Vortex is shattered, seemingly draining its power away. In the aftermath, Ronan retreats, while J'son's legions pull back. Meanwhile, Mantis joins on as a formal member, and after helping to recover the shards of the Black Vortex, Moondragon is taken on as well. It's also revealed that J'son was acting on the orders of Odin. With his "setback", Odin declares Midgard off limits from all other mystical/mythic realms/dimensions.



The Barrier

With Odin's barrier now erected, the factions on Earth begin plotting ways to escape the coming doom at the hands of Cul. Everyone from the demons to the mutant teams to HYDRA begin making plans to escape Earth or fight against the barrier.

The last 2 Worthy arise.

Meeting up with Hel, SHIELD decides to form a truce with her to defeat the Serpent. To that end, they use the forge of Surtur to forge new weapons, using a name that was used against Cul before: the Mighty.

The Worthy Vs The Mighty

Cul's forces begin spreading fear through New York. To stop him, the Avengers deploy to defeat all Circle of 8 forces and each of the Worthy. As an alternate strategy, they also deploy Avengers with personal connections to the Worthy in order to use emotion to snap them out of their magical trances. Hawkeye fights Mockingbird's form. Jessica Jones almost breaks through to Luke Cage's form. Dr. Strange and Ghost Rider's form engage. Black Knight's worthy form fights a fellow excalibur member. Skadi battles Captain America as her hate for cap should be greater than the magic.

Having driven all the Worthy off, Cul then storms to the area around Avengers Tower, seeking to crush hope once and for all in fear. However, Thor and the Jane Foster Thor along with the SHIELD Agent arrive to do battle. After fierce blows, the Serpent takes his true form, but together the 3 kill him at last. However, the battle was too fierce, and both Thors fall into "death". However, Odin then arrives on Earth, revealing he created the barrier as a way to keep the Serpent and the Incursions contained. He also reveals the Thors are just in an "Odinsleep", waiting to recover from their wounds.

Odin then challenges Earth to a battle for its survival, saying that the Incursions are too dangerous to allow Earth to live, intending to use the armies of Asgard to destroy all to save the Nine Realms. However, Iron Man challenges Odin to trial by combat, taking the Agent and 1 other hero in 3 rounds of battle against Odin. Using the Mighty weapons and their courage, Odin is driven off, begrudgingly giving the Avengers leeway to solve the Incursion crisis.

With the Fear crisis temporarily halted, SHIELD takes stock of their new priorities: figure out the Incursion problems, and find the missing "Worthy" heroes.

The Final Mission