Heroes
The Storyline is one where Apocalypse, Mandarin, Doctor Doom, Viper and Zemo have teamed up to take over the world. To this end, they've hired a number of mercenaries to do their bidding, forcing the heroes to band together for one massive battle.
Eventually, Doctor Doom and Zemo defect to the heroes when they realize that Apocalypse, Mandarin and Viper aren't going to make the world a better place once they rule it.
The problem is that this requites a larger roster for 16 heroes and villains each to allow room for members of the X-Men, Fantastic Four and Avengers to appear.
1. Iron Man (War Machine as alt skin)
2. Wolverine
3. Storm
4. Captain America
5. Spider-Man
6. Hulk
7. Cyclops
8. Black Widow
9. Ms Marvel
10. Luke Cage
11. Thor
12. Psylocke
13. Thing
14. Deadpool
15. Invisible Woman
16. Gambit
Villains
1. Apocalypse
2. Mandarin
3. Juggernaut
4. Zemo
5. Venom
6. Doctor Doom
7. Madam Masque
10. Sabertooth
11. Mysterio
12. Moonstone
13. Zeke Stane
14. Mercy
15. Viper
16. Spider-Slayer
DLC
Heroes
1. Daredevil
2. Doctor Strange
3. Punisher
4. Wasp
5. Blade
Villains
1. Sinister
2. Loki
3. Ultron
4. Magneto
5. Annihilus
Stages
Richard's Lab
New York Alley
Avengers Mansion
X-Hangar
Danger Room
Stark Industries
SHIELD Hellicarrier
Latveria
Hydra Base Upper Level
Hydra Base Lower Level
Abandoned Research Station
Apocalype's Tomb
Now when it comes to the story mode, I can see the chapter running in this order.
Chapter 1: Spider-Man
Spider-Man swings across New York City and sees Alistair Smythe attacking the Baxter Building. Spider-Man immediately stops him. Venom then appears and tells Spider-Man that Spider Slayer was his alone to defeat. Naturally, they fight. After defeating Venom, Mysterio comes by and tells Spider-Man that somebody is willing to pay a lot of money for Reed Richard's new invention but he's been waiting for a grudge match against Spider-Man for a long time. Spider-Man knocks Mysterio out and he and Venom bring him to the Fantastic Four for questioning. That's when Reed Richards tells Spider-Man that a great conspiracy is brewing and Spider-Man needs to stop it.
Spider-Man then enters a dark alley where his spider sense tells him that danger's nearby. Viper and Doctor Doom arrive and discuss how even though the attempt to steal Richard's new machine was a failure, Viper is willing to buy nuclear weapons from Doom. That's when Juggernaut ambushes Spider-Man as he's now working for Hydra. Viper and Doom escape during the fight and Juggernaut gets away.
Chapter 2: Deadpool
Deadpool arrives at the Avengers Mansion and rings the doorbell. Captain America answers and tells Wade that he's already been banned from the premises and isn't welcome. Deadpool then tells Captain America that he's not here to join the Avengers, he's here to KILL them because Mandarin is paying him a LOT of money. Deadpool fights Captain America but before he can kill Cap, Spider-Man intervenes. After also defeating Spider-Man, Ms. Marvel shows up, also fights Deadpool but Deadpool relents after Ms. Marvel tells him that she ordered Mexican food and Deadpool can have some if he assists the Avengers in fighting Hydra. Deadpool accepts the offer and then tells them that another mercenary was hired by Hydra to kill off the Avengers. That's when Madam Masque shows up, only to be bested by Deadpool. Deadpool then tells Madam Masque that he quits
Chapter 3: Storm
Storm is shown training in the Danger Room against Wolverine. After soundly defeating him, Sabertooth bursts in and attempts to kill Storm. Storm knocks Sabertooth out and then rushes to the X-Hangar where Juggernaut is seen fighting Domino who's bullets are ineffective. Juggernaut replies with, "Silly *****, your weapons cannot hurt me, I'm the Juggernaut!" Storm then says, "but this can" and blasts him with a gust of wind. After a fight with Juggernaut, Storm sees Apocalypse enter who then threatens her and the X-Men with complete destruction. Storm then leads the charge against Apocalypse and after fighting him, realizes that he's simply too strong to take on as the X-Men need backup. Beast, Domino, Rogue and Northstar stay behind to defend the X-Mansion while Storm, Gambit, Wolverine Cyclops and Psylocke are to link up with the Avengers to defeat Apocalypse.
Chapter 4: Black Widow
Black Widow is aboard the SHIELD Helicarrier talking about the recent attacks on the Fantastic Four, X-Men and Avengers with Falcon and Diamondback. That's when Nick Fury calls her in to warn her of an immanent attack on SHIELD. Black Widow then looks out the window and sees Hydra operatives assaulting the Helicarrier. She gears up and then cuts through multiple Hydra soldiers before doing battle with some of Hydra's hired mercenaries. After defeating both Mercy and Moonstone, Black Widow faces off against Zemo who's leading the Boarding party. After also defeating him, Zemo retreats with his mercs and any Hydra agents still alive. Black Widow then contacts Captain America and declares a summit between the Avengers, X-Men, Fantastic Four and SHIELD at the Avengers mansion. Once there, Doctor Doom enters and attacks the heroes before Black Widow defeats him only to realize that it's a Doombot and not the real Doom. The Doombot then explodes and levels the mansion.
Chapter 5: Iron Man
Tony Stark's cell phone shows over 20 missed calls while Tony lays in bed. That's when War Machine knocks on his window before simply deciding to crash through it to wake Tony up. War Machine explains that the United States is being threatened by multiple supervillains and Iron Man is needed to save the day. Naturally, Iron Man falls back asleep. Then when Ghost, Madam Masque and Iron Monger 2.0 show up, Tony finally wakes up, dons his armor and tells War Machine to handle Ghost while Iron Man takes on the other two. After defeating Madam Masque, War Machine blows Ghost right through a wall. That's when Zeke Stane hacks War Machine's armor. Tony then is forced to fight War Machine. After beating him, he faces down Iron Monger 2.0 but the celebration is not to last. Mandarin appears and tells Iron Man that he's lost already and that his friends are all doomed. Iron Man and Mandarin do battle but in the aftermath Mandarin reveals that he has a bomb and has mind-controlled Pepper with her already in Hydra custody. Iron Man and War Machine jump out of the building onto the street below as Stark Industries explodes.
Chapter 6: Luke Cage
Aboard the SHIELD Helicarrier, the heroes locate the villains in Latveria and prepare to land right inside Doctor Doom's palace. But that's when things have gotten out of hand. Mercy has located the heroes and Mandarin has used her intel to mind control them remotely. Luke Cage however isn't affected but is forced to fight Hulk, Gambit, Invisible Woman and Venom. After defeating all of them, they return to normal and prepare to assault Doctor Doom.
Chapter 7: Thing
Thing enters Doctor Doom's Palace and confronts Doom personally despite his guards getting in the way. Unfortunately, Doctor Doom is being guarded by Sabertooth, Mysterio and Mercy. He defeats all three of them and then moves in on Doom. After a long, drawn out battle, Thing gains the upper hand but Doom gets one cheap shot on him that brings him down for the count.
Chapter 8: Invisible Woman
Sue sees Ben crumpled on the ground and immediately takes revenge on Doctor Doom. That allows her to be attacked from the side by Iron Monger 2.0 and Spider-Slayer. Sue defeats both of them but then Juggernaut comes out of nowhere and protects Doom. Sue then defeats Juggernaut and then finally, FINALLY takes down Doctor Doom. Seeing as his own allies have fallen, Doom surrenders and allows the heroes to take him into custody. Wolverine refers to Doom as a, "coward." Doom replies with, "Not a Coward. Intelligent. Doom knows when to fold."
Chapter 9: Zemo
Baron Zemo talks to Viper about the loss of Latveria and the final endgame. Viper replies that she hopes to punish any territories that resist harshly and will nuke them anyone once they're secured. Zemo is deeply bothered by this and the two come to blows. Zemo defects from Hydra, claiming that it's not the same under Viper and barely escapes with his life. He then escapes into an antarctic research base and tells the heroes to meet him there. Cyclops claims that it's obviously a trap but Captain America argues that at least it's a lead. The Helicarrier heads to Antarctica where Zemo faces the heroes. Cyclops and Psylocke defy Captain America and attack Zemo. Zemo manages to beat both of them, but not Captain America's angry and wants to face Zemo himself. Zemo defeats Cap and then explains that this is going to be one long, difficult battle against impossible odds. Wolverine replies that he's known as the best at what he does for a reason and Cyclops reluctantly relents.
Chapter 10: Hulk
Once at the base, Hulk defeats multiple Hydra guards. That's when Hulk goes entirely berserk and turns on his own teammates. Hulk takes on Black Widow, Luke Cage and Deadpool with Deadpool saying, "Hey, if anyone's here is allowed to kill their teammates, it's me." Hulk defeats all three of them and storms off to fight Mercy. Hulk naturally wins.
Chapter 11: Cyclops
Cyclops chases Apocalypse through the Hydra base and corners him. The two of them fight, after which Apocalypse escapes and Cyclops is cornered by Moonstone, Mysterio and Spider-Slayer. He defeats all of them and then waits for Captain America's orders.
Chapter 12: Psylocke
Psylocke encounters Hulk in a rage. She immediately fights him off which causes him to return to normal. That's when Spider Slayer and Zeke Stane show up. Psylocke defeats all of them. Mandarin then appears out of nowhere. After it appears that Psylocke has finally won, Mandarin mind controls her which causes the player to switch to Iron Man for one fight against Mandarin. Iron Man wins and forces Mandarin to tell him Pepper's location. Tony and Pepper are reunited.
Chapter 13: Captain America
Cap fights Madam Masque and Apocalypse. Masque is defeated but Apocalypse escapes. Captain America then sees Viper who's gloating about how she's already won. Captain America defeats her and she then confesses that Apocalypse already has the nukes and he's taking them elsewhere and he's kidnapped four of their teammated to be a new Four Horsemen. Zemo then criticizes Cap's leadership which cases a fight to break out between the two of them. Cap wins and gives Zemo a warning to not challenge him again.
Chapter 14: Thor
As the team laments that they've lost their chance at stopping Apocalypse, Viper refuses to give the heroes any intel and Zemo claims that he was kept in the dark, Thor comes out of nowhere and says that Odin foresaw great destruction and having shared in his vision, Thor knows where Apocalypse is. However, Thor can only take one other hero to fight Apocalypse. Wolverine volunteers to go with Thor and the two head to Egypt into the tomb of Apocalypse. Upon arriving in the caverns leading to Apocalypse's lair, a new four Horsemen arrive who were heroes that Apocalypse kidnapped. After fighting Ms Marvel, Invisible Woman, Storm and Thing, Thor decides to head for the Nukes while Wolverine takes on Apocalypse.
Chapter 15: Wolverine
Wolverine arrives in Apocalypse's chamber where he's encounters a Doombot in Iron Man armor. Wolverine defeats it, then he's ambushed by Sabertooth. Doctor Doom walks out and mentions that the heroes were fools to leave him alive. Wolverine tells Doom that without Captain America calling the shots, he does plan on killing Doom. Doom states that it's always been his plan to overthrow Apocalypse and claim the world for himself and Wolverine only needs to join him to make the world a utopia under Doom's rule. Wolverine doesn't buy it and the two battle, after which Doctor Doom teleports away before Wolverine can kill him. That's when Sabertooth appears out of nowhere and grabs Logan from behind. Apocalypse thanks Wolverine for getting Doctor Doom out of the way for him and orders Sabertooth to kill Wolverine. Meanwhile, Thor tosses the nukes into the ocean where nobody can be hurt. Wolverine breaks free of Sabertooth's grip and the two fight with Wolverine seemingly killing Sabertooth. That's when Apocalypse mentions that he's now at full power and he's ready to prove that Wolverine is indeed mortal. In this form, Apocalypse has enhanced health,damage and speed. Wolverine then proceeds to kill Apocalypse once and for all, however he spots a trail of blood from where he killed Sabertooth, proving that he's not dead yet.
After the credits, Sabertooth mentions that everyone else is dead now and the world now belongs to his boss. Sinister appears out of the shadows smiling
: Rogue Black Widow Colossus Vision Mystique Blob Enchantress Super Skrull 
