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"A mysterious Pulse has slammed into the Earth, wreaking havoc worldwide. As a new S.H.I.E.L.D. recruit, you must prove yourself far earlier than intended, restoring order to a New York under siege by opportunistic criminals of every stripe."
— Chapter Briefing
| Mission 1 - The Hydra's Tail | |
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| Mission 2 - Class is in Session | |
| Mission 3 - HAIL HYDRA! | |
| Mission 4 - Designed Only for Killing | |
| Mission 5 - O Brother, Where Art Thou? | |
| Premium | Mission 6 - Extra Large |
Mission 1 - The Hydra's Tail[]
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"Hydra forces, led by Viper, appear to be after a mysterious energy signature."
— Mission Preview
Unlock Requirements: Complete Tutorial
Location: Meatpacking District
Team-Up: Hawkeye
Low: x2
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Minimum Cleared: 2
Team-Up: Hawkeye
Boss Drops: Single-Shot Thumper, Hidden Blade
Challenge Mode Boss Drops: Custom D.A.R.S. Suppressor
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Mission 2 - Class is in Session[]
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"One of Viper's men escaped with a package that contained the energy signature you were after. You've traced it to an area where R.A.I.D. troops have been deployed with Whiplash leading them."
— Mission Preview
Unlock Requirements:
Complete 1 Star Mastery in Chapter 1 - Mission 1
Location: Empire State University
Team-Up: Iron Man
Low: x2
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Minimum Cleared: 3
Team-Up: Iron Man
Boss Drops: Remote Jet Injector, Precision Focus Aperture
Challenge Mode Boss Drop: Custom NF3000
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Mission 3 - HAIL HYDRA![]
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"Hydra still hasn't given up, with Baron Zemo leading his men on a rampage through Chinatown."
— Mission Preview
Unlock Requirements:
Complete 1 Star Mastery in Chapter 1 - Mission 2
Flight Deck: Own and staff 2 Jets
Location: Chinatown
Team-Up: Captain America
Low: x1
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Medium: x3
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Minimum Cleared: 3
Team-Up: Captain America (Optional)
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Minimum Cleared: 5
Team-Up: Captain America
Boss Drops: Knuckle Sting, B&F MP-2
Challenge Mode Boss Drop: Custom Sgt's Fury
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Mission 4 - Designed Only for Killing[]
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"A.I.M. forces and an unknown presence threaten the Financial District."
— Mission Preview
Unlock Requirements:
Complete 1 Star Mastery in Chapter 1 - Mission 3
Location: Financial District
Team-Up: Black Widow and Thor
Low: x1
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Medium: x1
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High: x1
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Minimum Cleared: 2
Team-Up: Thor (Optional)
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Minimum Cleared: 4
Team-Up: Black Widow
Boss Drops: Nano-nurse, Sub-0 Optics Military Rifle
Challenge Mode Boss Drops: Custom Survival Knife
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Mission 5 - O Brother, Where Art Thou?[]
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"The chaos of the Pulse has attracted the attentions of a certain Trickster and his minions. The Avengers Mansion is threatened and S.H.I.E.L.D. must intervene."
— Mission Preview
Unlock Requirements:
Complete 1 Star Mastery in Chapter 1 - Mission 4
Location: Avengers Mansion
Team-Up: Thor
Low: x2
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Medium: x3
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High: x2
Minimum Cleared: 4
Team-Up: Thor
Boss Drops: Chain Blade, Precision Focus Aperture
Challenge Mode Boss Drop: Custom R-Pod Concealed Cutter
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Premium Mission: Extra Large[]
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"Hulk Smash Mysterious Device!"
— Mission Preview
Unlock Requirements: Recruit Hulk for 90 
Location: NY Public Library
Team-Up: Hulk
Note: Mission difficulty scales to players' agent level
Medium: x5
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High: x1
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Team-Up: Hulk (Optional)
Minimum Cleared: 4-5
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Minimum Cleared: 6
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Minimum Cleared: 8
Team-Up: Hulk
Boss Drops: Gamma Booster, Gamma Gadget
Challenge Mode Boss Drop: Gamma Gadget, Custom B&F "Highroad"
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| v · e | |||
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| Prologue (Dialogues) | |||
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1. The Hydra's Tail 2. Class is in Session 3. HAIL HYDRA! 4. Designed Only for Killing 5. O Brother, Where Art Thou? Premium Mission: Extra Large |
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1. In the Family 2. The Sound of Feathers Ruffling 3. Step into the Shadows 4. Mean People 5. Mutate or Die Premium Mission: Ulterior Motive |
| Dialogues | Dialogues | ||
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1. Sacred Ground 2. Brooklyn Bridge is Falling Down 3. RAID-ical Resolution 4. Odd Bedfellows 5. Three Strikes Premium Mission: Cephalocarrier |
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1. Jailbreak 2. Center Point 3. Hydrophobia 4. Unexpected Guest 5. Command Performance Premium Mission: Tooth and Claw |
| Dialogues | Dialogues | ||
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1. An Early Frost 2. Taking AIM 3. Chemistry Set 4. Desecration 5. City of Stone Premium Mission: Hydra Assemble! |
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1. Underworld Masquerade 2. I Predict a Riot 3. Tentacular 4. Mutants Marching 5. Magic Hand Premium Mission: Jailhouse Rock |
| Dialogues | Dialogues | ||
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1. Anticipation 2. Taking It to the Streets 3. Head Shot 4. Deceiver and Destroyer 5. Chaos Reigns Premium Mission: A Whole New U |
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1. Enemies Hand in Hand 2. Congressional Action 3. Grand Experiment 4. Quis Custodiet 5. Regeneration Premium Mission: Bring the Thunder |
| Dialogues | Dialogues | ||
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1. The Boss is Back 2. Mutatis Mutandis 3. Hand and Fist 4. Weird Science 5. Criminal Minds Premium Mission: Darkness Rising |
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1. U-Foe Sighting 2. Power Play 3. Stormy Weather 4. Grinning Skull 5. The Syndicate Premium Mission: Der Rote Schadel Lebt Noch |
| Dialogues | Dialogues | ||
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1. Mutants Take Manhattan 2. HYDRA for Humans! 3. Enter the Circle 4. Underground Resistance 5. Mutation Zone Premium Mission: Breaking the Syndicate |
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1. Lokasenna 2. Ouroboros 3. Under the Hood 4. Technocrats 5. Feeding Frenzy Premium Mission: Doom's Day |
| Dialogues | Dialogues | ||
| v · e | |||
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1. Artificial Sweetener 2. Trans-Atlantic 3. Sword in the Stone 4. Vulture, MP 5. God Save The Queen Premium Mission: To Catch a Thief |
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1. Antiquity 2. Eight Fingers 3. Foggy Vision 4. The Sting 5. Rehabilitation Premium Mission: Rock Candy |
| Tasks • Dialogues | Tasks • Dialogues | ||
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1. Shattered 2. Gates of Hell 3. Capo Crimine 4. Growing Pains 5. Techno Illogic Premium Mission: Punishment |
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1. Splintering Cells 2. Heated Negotiations 3. Tourist Trap 4. Circular Speculations 5. Lockdown Premium Mission: On the Prowl |
| Tasks • Dialogues | Tasks • Dialogues | ||
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1. Tech Up 2. Grudge Match 3. Up a Tree 4. Cleaning House 5. Enchanted Premium Mission: Deific Inadequacy |
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1. Unknown Intel 2. Ancient Knight 3. Dark Complications 4. Harvester of Souls 5. Clash of Titans Premium Mission: Fourth Wall |
| Tasks • Dialogues | Tasks • Dialogues | ||
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1. Black Queen, Black Knight? 2. Mysteries Abound 3. Savage 4. Many Heads 5. But One Immortal Premium Mission: Explosive Events |
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1. Sentinel City 2. We're Not Worthy! 3. Highest Bidder 4. Demonic Dealings 5. Mindless Mischief Premium Mission: Savage Science |
| Tasks • Dialogues | Tasks • Dialogues | ||
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1. Ritual Cleansing 2. Delusions of Grandeur 3. The Better of Both Worlds 4. Change the Channel 5. Hammer Hunt Premium Mission: Worlds Domination |
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1. Breaking into Vibranium 2. The Big Apple 3. Madripoor 4. Eternal Darkness 5. Cosmic Connections Premium Mission: I Have Become Death |
| Tasks • Dialogues | Tasks • Dialogues | ||
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1. Hellfire Extinguisher 2. Incurring Incursions 3. Soul Searching 4. Devil's in the Details 5. Forging Alliances Premium Mission: Tower's Avenger |
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1. The Worthy Appeal 2. Time Trials 3. Serpent Strike |
| Tasks • Dialogues | Tasks • Dialogues | ||