There are a total of 12 levels or "bonus stages" in LEGO_Marvel_Super_Heroes. They have comic style intros and outros, narrated by Deadpool. Other than "The Brick Apple", each level has a hidden Deadpool brick (Red brick) which can be bought from his room on-board the S.H.I.E.L.D. Helicarrier. These levels can be accessed by finding a doorway somewhere in Manhattan, all of which are marked on the map, like the normal levels. For "The Brick Apple", the door is in the base of the Statue of Liberty, for the others, they are near the level's location. Similarly to other games, most of these doors have to be constructed before being entered, and some have other things that have to be done.
The following is a list and description of each bonus stage:
|Level||Playable characters||Location||Enemies||Bosses||How to unlock|
|The Brick Apple||
Manhattan (in LEGO form)
|None||None||Finish the Story|
|House Party Protocol||
|None||Finish Story Mode|
|Tabloid Tidy Up||
The Daily Bugle
|None||None||Collect 10 Gold Bricks|
|Nuff Said||Marvel H.Q.||
||Collect 20 Gold Bricks|
|A Shock Withdrawal||Bank||
||Collect 30 Gold Bricks|
|Feeling Fisky||Fisk Tower||Collect 50 Gold Bricks|
|Put Up Your Dukes||Fogwell's Gym||None||Collect 75 Gold Bricks|
|Stunt Show Surprise||Circus||
||Collect 100 Gold Bricks|
|Reptilian Ruckus||Reptile House||None||Collect 125 Gold Bricks|
|Stranger Danger||Haunted House||
||Collect 150 Gold Bricks|
|The Thrill of the Chess||Ferry||
||Collect 175 Gold Bricks|
||Collect 200 Gold Bricks|
- Spider-Man is playable in 4 levels, while Captain America and Iron Man are playable in 2 levels.
- The Brick Apple and Tabloid Tidy Up are the only levels to not feature boss battles.
- The Brick Apple, Tabloid Tidy Up, The Thrill of the Chess and Bro-tunheim are the only 4 levels where you play as the villains.