This is where the
EXG secrets are revealed. Just press the spoiler tag to view each of them.
HelicarrierSpoiler Crew Quarters: This is the new stage that you get to after defeating

Bullseye and destroying the missile in the Command Deck. If you're already familiar with the Helicarrier simulator mission, then you know that in this stage, you have to break the broken wall in the room to the right of the forcefield to get across.
Omega BaseSpoiler Omega Exterior: You know the first door behind you when you start leads back to the stage you came from, Wrenchworks. But, the other doors lead somewhere as well! The 2nd door leads to the new stage,
Logistics Facility. The 3rd door leads to another new stage,
Level 3, but you have to play through the Project Labs to unlock it. And the 4th door is locked at first.
Level 3: There is a special conversation if

Mr. Fantastic is on your team; Throw objects or enemies into the walls to break your way through the area; The

Hulk is very dangerous, so a constant collective effort is needed or he'll kill you. Keep attacking him from far. If the character runs short in health, switch to another; There is a special conversation if the

Thing beats the Hulk.
Top Deck: Once you start there, move to the left. You'll notice that you can return to the Omega Exterior via the Executive Elevator. That's what the 4th door was and is now unlocked.
AtlantisSpoiler No secrets added there.
Valley of SpiritsSpoiler Golden Court: Defeating the Grey Gargoyle will unlock the "Stone Cold" objective.
New York CitySpoiler Greenwich Village: There is a special conversation if

Luke Cage is on your team; Anyone with Might can lift and throw the cars; There is a Mysterious Cache to the street west of the starting point. You'll find it next to a police officer and a vending machine -- you'll notice these chests have my symbol on them; There's a special conversation if

Daredevil talks to Bullseye; After you defeat

Bullseye, go to the subway entrance nearest to you to reach the next stage.
23rd Street: Anyone with Might can lift and throw the cars; Talking to the police officer there will unlock the "Police Briefing" objective. There is a special conversation if

Spider-Man talks to the police officer; There is a Mysterious Cache in one of the north 'hood areas just after the extraction point.
Park Avenue: Anyone with Might can lift and throw the cars; There is a Mysterious Cache all the way north from the starting point, at the farthest northeast corner; You have to examine a rather large limousine to the west of the stage near the hotel to shut down the forcefield stopping you from advancing. Move up the debris to the left of the hotel and follow that path to find a Skill Point / secret area.
Manhattan Skyline: At the far north end of the stage where the stairs are, go left to find one enemy there. Jump over the rooftop air machines to find a Skill Point / secret area; There are four Mysterious Caches to the east of the wooden plank to that area; After your initial talk with Senator Leiber (Stan Lee), don't go back to the Sanctum Santorum yet -- there are special conversations if

Captain America,

Spider-Man,

Thor,

Wolverine,

Iron Man,

Hulk, or

Deadpool talks to him a second time.
MurderworldSpoiler Big Top: The arcade machine to the right of the starting point can take you back to the fake "Castle Doom" if you missed something there; The arcade machine to the left is locked initially. Break the dunk tank and you'll hear a chime, unlocking the left arcade machine, which takes you to the secret stage,
Murder Midway.
Murder Midway: There is a special conversation if

Hawkeye meets Swordsman.
Mephisto's RealmSpoiler Hall of Zarathos: This is the new stage you get to after defeating

Blackheart and make the choice of who to save. There are two treasure chests there. Once you enter the Gate of No Return, you cannot return back to the previous areas of Mephisto's Realm, so do all of your exploring before then.
Bifrost BridgeSpoiler Bifrost Bridge: Enter the Viking ship to go to the new stage, Frigga's Valley, which has a lot of upgrades.
Frigga's Valley: When you break the first door and go through the doorway, there will be four body upgrades to the right, and four striking upgrades to the left; Go along the left path and you'll see three large stones to the left -- break them to find a Skill Point / secret area; After you break the second door and go through the doorway, there are four treasure chests around the section; Go to the far right outside of this section to find four focus upgrades; Interact with the Odin statue in the north center to unlock the "Eye of The Storm" objective.
AsgardSpoiler No secrets added there.
NiffleheimSpoiler No secrets added there.
Shi'ar StarshipSpoiler Science Section: Rescuing Princess Lilandra by breaking that torture device will unlock the secret new mission,
Astral Plane! When you return to Attilan, enter the portal near

Black Widow.
Astral PlaneSpoiler Shadow Gallery: There is a special conversation there if

Doctor Strange is on your team; There is a striking upgrade to the west of the area after the second staircase.
Forsaken Place: There is a special conversation there if

Storm is on your team; There is a body upgrade in one of the areas with multiple enemies.
The Endless Stairs: There are two special conversations if

Professor X is on your team; At some point during the stage, you'll run into a focus upgrade; Each of the four Orbs of Darkness around the area where you fight the Shadow King will greatly enhance the hero that grabs each of them. You can grab each of them during the Shadow King fight to help you if you wish, though that's somewhat cheap.
Skrull HomeworldSpoiler Sky Towers: After destroying the three towering generators, examine the large gaping hole in the center of the last area. This will unlock the secret stage,
Andromeda Reseach Labs.
Andromeda Reseach Labs: There are five consoles around this stage. When you go outside the starting room, the console to the right has a conversation if the

Thing activates it. The console to the left has a special conversation if

Invisible Woman activates it. The console near the missile-looking objects in the next area has a special conversation if

Human Torch activates it. Then, the large console in the next room has a special conversation if

Mr. Fantastic activates it. Activate all five consoles to unlock the "Lab or Prison?" objective; When the jet to the southwest of the bridge area to trigger short dialogue, which then unlocks the way back up to the Sky Towers when you're done there.
Time WarpSpoiler Egypt: There is a special conversation if

Moon Knight is on your team; There is also a special conversation if

Magneto meets

Apocalypse; There are large golden chests around this stage. While they don't open, they act as caches triggering health, energy and items; Defeat Apocalypse to unlock one of the gates leading to the next portal.
Asteroid M: There is a special conversation if

Magneto is on your team; Break the wall north of the glowing bridge to progress on through the space station; There is a special conversation if

Scarlet Witch meets Magneto; The Master of Magnetism is one of the toughest opponents in the game -- roll when he fires any beam attacks. If he uses his forcefield too much, at some point it doesn't work anymore -- that's when he becomes easier. Do not attack him while the forcefield is active, as some powers are reversed back at you.
LatveriaSpoiler Latverian Warship: There is a special conversation if

Iron Man is on your team; Destroy the crates near the Doom Iron Men generators to shut them down, but you can use them to gain more XP, as each pod launches up to 15 of them, so that's 30 for each generator; There is a focus upgrade up the stairs near where the forcefield is at the end of the boat.
Prison Compound: There is a special conversation if

Iceman investigates the Blackbird to the right of the starting area; There is also a special conversation if

Magneto or

Psylocke confronts Lucia von Bardas & Dark Wolverine; The latter is extremely dangerous, so take out Lucia von Bardas first so you can't get stunned and become easy prey for him to kill you; There are hidden body & striking pickups if you go inside the large crates; The last Doom Iron Man with a powerup has the keycard needed to enter the large door -- this will lead you to Castle Doom.
Castle DoomSpoiler Castle Doom: There is a special conversation with Victorious if

Human Torch is on your team; Defeat her to complete the new objective and unlock the extraction point & Doom's Portal.
Stark TowerSpoiler The elevator-looking platform near Wyatt Wingfoot has a glowing

there. This will lead you to the X-Mansion!
X-MansionSpoiler Xavier Institute: There are three elevators leading to the X-Men HQ in the sub-basement: One is the wooden block just below the main staircase, one is the wooden block next to the TV in the Rec Room, and one is the wooden block in the back of the Classroom; The pictures on the walls are "firsts" -- the X-Men's first comic book, first video game, and first movie; If you move close to the TV in the Rec Room, it will show a screen of "X-Men: Children of The Atom," one of my favorite games; Go to the front door near the staircase to return back to Stark Tower.
X-Men HQ: There is an Energy Replenishing Machine in

Beast's lab, and a Health Replenishing Machine in the medical facility; There is a Skill Point located in the Brig. Just shut off the forcefield control to access it; The Danger Room stage's enemies will respawn each time you go there, so you can gain XP, but you can't gain reputation points after the first time.
Sanctum SantorumSpoiler Get the "Gem of Oshtur" to the left of the starting point, then speak to the Ancient One at the mirror of the next room to the right. It will unlock the new secret mission, New York City! Now just go back to the starting room area and access the front door.
ValhallaSpoiler Speak to Hermod and Sif to unlock objectives. However, if you unlock one of them, you can't unlock the other until you complete either the Bifrost Bridge or Asgard mission first.
AttilanSpoiler No secrets added there, except for the one mentioned in the Shi'ar Starship mission.
Doomstark TowerSpoiler You can access the Iron Man Lab at any time now by going to the waterfall; Speak to

Vision and ask him if there are any Super Heroes left on Earth. At some point, you'll see a time rift -- a tear in the space/time continuum. Enter that portal to play the new secret mission,
Time Warp!; Have

Nick Fury take you to Castle Doom as normal -- you'll land in the new mission,
Latveria instead!
Iron Man Lab: After facing the multiple Doom Iron Men, there is a new boss fight -- Dark Iron Man! There is a special conversation if

Ms. Marvel is on your team and confronts him.