Several years ago, a gigantic island arose from the southern Atlantic Ocean due to sudden shifts on the Earth's surface. Numerous adventurers made their way to the island to investigate, but none of them were able to return home safely. This island was named Atlantis, and nobody approached it out of fear. The game's main character is an amateur adventurer named Wynn, who decides to go to the island after learning that his master disappeared on the island over half a year ago. Armed with the special dynamite invented by the master, Wynn heads over to Atlantis all by himself to face an evil emperor who seeks to revive an ancient empire.
The game is a side-scrolling platform game, similar to Super Mario Bros., but unlike Mario, it is possible to scroll in both directions on the screen rather than just the right-hand direction. However, the somewhat choppy physics of Atlantis no Nazo, one-hit deaths, and multiple pathways make it much more challenging than Super Mario Bros.
The levels in the game are referred to as "zones", and the player travels through various locations such as fields, caves, ruins, temples, and even across clouds. The games consists of 101 of these zones (zones 1-99, the final zone, and secret final zone), and features not native to Atlantis, such as Moai face statues and pyramids appear in backgrounds of the zones. In later zones, the terrain may be difficult to see because of the dark, or it may become hard to control the character because the ground is covered with ice. Some zones (called "black holes") only involve falling. Three zones are not connected to the main game, so they can only be accessed using a hidden command that allows the player to select and play any zone they want.
The player starts from the first zone, and must head towards the final zone to rescue Wynn's master while fending off numerous enemies by throwing sticks of dynamite. The player warps into different zones by going into the entrances placed within each zone. However, the zones do not come in numerical order, as several warp entrances may be placed within a single zone.
The earlier zones are generally easier in terms of difficulty, and the later zones are more difficult. Certain entrances may take the player from an easy zone directly into a harder one (with secretive warps jumping the player by a great number of zones), or vice versa. A time limit exists for each level, and the timer displayed on the lower part of the screen begins counting down from 999 all the way to 001 followed by OUT. Failing to reach the next zone during the time limit results in a loss of one life. The player also loses a life if their character touches an enemy, gets hit by an enemy attack, falls into a pit, or is caught in the explosion of their own dynamite stick. The game over screen appears once the player has no lives remaining.
Items that aid the player can be found in certain locations in each zone. Item effects continue up until the player loses a life, but certain ones may last even longer. The items the player currently has are displayed at the start of each level. The light-bulb item causes the screen to light up in dark areas whenever Wynn throws a stick of dynamite. The shoe item allows Wynn to walk on clouds, and the "S" item causes damage to all of the enemies on the screen whenever he throws a stick of dynamite, even if it falls into a pit or goes off-screen. The "↑" item causes the player's points to increase by 3 points whenever the player presses up on the keypad. The "2" item causes defeated enemies to yield points and the value of treasure boxes to double. The clock item slows the timer countdown, and the microphone item allows the player to stop enemy movements by speaking into the second controller's microphone. The star item causes Wynn to become invincible to enemies and projectiles, but the player can still lose by falling into a bottomless pit or running out of time.
As explained before, it is possible to warp to other zones through the entrances located within each field. Open entrances can be entered directly, but closed entrances need to be opened first by exploding a stick of dynamite before they can be entered.
Hidden warps can also be done by exploding dynamite in certain locations to cause hidden entrances to appear, falling into certain pits, suicide bombing in certain locations, or jumping into certain spaces. Suicide bombing is a technique that takes advantage of the game's system where Wynn falls downwards across the screen whenever he gets caught in the explosion of his own dynamite. The player does not lose a life until Wynn completely disappears off the screen, so it is possible to fall into previously inaccessible areas and entrances via suicide bombing. However, the player loses the light-bulb item whenever they try to suicide bomb, even if it results in entering another zone.
Numerous treasure chests are located within each zone, and awards the player a bonus between 1-1,000,000 points. Items are never found within these chests, and the points are doubled if the player has the "2" item in their inventory. There are 200 chests in total, and the number of chests the player collected is displayed on the game over screen. However, it is impossible to collect all 200 chests during a single play-through because some of the zones are inaccessible unless the player uses the zone selection hidden command. The player gains one extra life every 100,000 points gained, but no extra lives are rewarded if Wynn opens a treasure chest that awards 1,000,000 points.
In the 20th zone, there are 3 Moai face statues placed next to each other, and the message "KEYWORD-NAGOYA-" is displayed on the screen. This is a code for the numbers 7, 5, and 8 (NA=7, GO=5, YA=8) and the player can warp to the final zone if they throw dynamite 7 times on top of the left statue, 5 times on top of the middle statue, and 8 times on top of the right statue. However, this final zone is structured differently from the one accessed without using the warp, so it is called the "secret final zone" or "hidden final zone". A large bonus of 4,000,000 points is rewarded if the player passes in front of the devil's statue located at the center of the level. In the Super Pitfall II version, the NOGOYA has been changed to 7 5 8 and the secret final zone gives you the maximum amount of lives as wells as all the power ups in the game.
The black hole is an eerie area in zone 42 which is completely dark and will automatically take the player to the game over screen. Wynn falls downwards as the message "BLACK HOLE!" is displayed in the background. There are no footholds, and it is impossible to escape unless the player entered the zone selection secret command beforehand. If the player has gained infinite lives using a cheat, they can never reach the game over screen, and can never escape from the black hole zone. Another black hole entrance may appear in zone 29 depending on the player's warp route, probably due to a programming bug.
The backgrounds of zones 57 and 94 flash with green and red color, respectively. These flashing effects were removed when the game was later ported to the PlayStation and Windows systems after Pokémon Shock revealed the possibility of photosensitive epilepsy in television and video games.
Zones 55, 59, and 84 are not connected to any of the other zones, and are impossible to access unless the zone selection hidden command is used. Though a hidden entrance to zone 59 does exist in zone 50, its location is overlapped with a block, making it impossible to enter. There are also several items that do not appear at all in the game, but exist in the game's data. It is unclear why these zones and items remained in the final version of the game.
In the game's characteristic dark zone, the terrain becomes invisible due to the dark background, but the player's character and enemy characters remain visible as in all other levels. However, in the game's data there is also a program that causes enemy characters to become less visible in dark levels as well. However, this would increase the game's difficulty even more to make the level far too difficult, so this system was never used in any part of the game.
Wynn's master is being held captive in the final level of the game (this is different from the secret final zone accessed with the NAGOYA warp), which is also the main base of the evil king Zavila, who attacks by shooting fireballs at Wynn. Though the last level is of extremely high difficulty, it can be completed easily if the player has the invincible star item (however, it may be equally difficult to get to the final zone with the star item still intact). Only 3 of Zavila's fireballs can be displayed on-screen at one time, so the player must progress across the level at the right timing if they do not have the star item. The attacks end and the master is freed when the player reaches the diamond-shaped object placed in the middle part of the level. Though this marks the conclusion of the game, there is no ending screen or staff roll (some credits do appear fairly early in the game in zone 26), and the master simply stands there laughing instead of showing any sign of escaping with Wynn. The game continues even after the conclusion of the final zone, and if the player advances to zone 99 in the second play-through, a new entrance appears which takes the player back to zone 6. The difficulty is increased significantly during the second play-through, but nothing is added to the gameplay other than the new entrance in zone 99. The game essentially continues on endlessly.
It is never made clear what the "mystery" of the island is, even after the player finishes the final zone. However, another mystery does appear in the final zone where it turns out that Wynn's master is Gonbe; the main character from Ikki, another video game developed by SunSoft.
The game is set in the mythical land of Atlantis. The player controls an amateur adventurer named Wynn (ウィン), whose objective is to save his master being held captive in the final level. SunSoft developed the game with the intention of surpassing the enormously popular Super Mario Bros., and advertised the game with the slogan Ano Super Mario wo koeta!! (あのスーパーマリオを超えた!!, lit. "The game that surpassed Super Mario!!" The number of levels included in Atlantis did surpass the number included in Super Mario Brothers).
Though the game was never released outside Japan, a partially translated version titled Super Pitfall II was under development by Activision for release in North America as the sequel to the unrelated Super Pitfall. The game was ported to the PlayStation on December 6, 2001 as part of Memorial Series SunSoft Vol. 2 (coupled with Route-16 Turbo). The game was also released for the Microsoft Windows operating system on June 29, 2001 as part of the Ultra 2000 Sunsoft Classic Games 1 (coupled with Super Arabian and The Wing of Madoola) and its value version, Yu Yu Sunsoft Kessakusen 1 (released July 2, 2004).
The protagonist Wynn made an appearance in Sunsoft's 2011 game Shanghai Musume: Majhong Girls.