On the screen is a randomly generated Super Mario level that, as the game progresses, autoscrolls progressively faster and spawns progressively more objects. Each object will despawn once it moves off of the left side of the screen. Players must ensure that no enemies despawn alive, no coins uncollected, and no blocks intact, by essentially tapping everything. If one of these objects despawns unscathed, the player will power down. Tapping empty space creates Boost Blocks, which abide by their NSMBU rules and limitations.
Throwable items can be dragged around the screen thanks to the Display's multitouch hardware. Simply releasing this drag will drop the item, similarly to how Mario would drop something by holding down and releasing the carry button. To toss such an item to the side, the player must "flick" it to the left or right, quickly moving their stylus, finger, etc. in that direction while lifting it from the screen.
The player has two item reserves that contain a Fire Flower and an Ice Flower at the beginning of each game. Their current state is indicated by the power-up icon in the upper-left corner of the screen. Certain power-ups are required to hit certain enemies; for instance, tapping a Spiny without a Fire Flower will cause the player to power down, whereas tapping one with a Fire Flower will put the Spiny in its fiery death throws. A power-up attack will only override the normal "jump" when possible, meaning that Buzzy Beetles and the like can be attacked even with the ineffective Fire Flower equipped. Power-ups need not be collected, but blocks that contain them must still be opened.
Checkpoint Flags can be tapped to let the player restart from that point. They will also power the player up to Super form if they do not already have a power-up. However, their points will roll back upon respawning, and both item reserves will empty. This is meant to introduce a risk-versus-reward gameplay mechanic, and due to this, the player is not required to tap Checkpoint Flags.
In the upper-right is the score counter, which increases based on the player's actions according to the same rules as in any New Super Mario Bros. game. However, unlike in those games, it is not capped and not useless. The high score is displayed below this in smaller print.
- Despite the title, the game has little in common with the SNES game Mario is Missing! or its sequel.
- Coins can be collected by dragging ones' stylus or finger across the screen. Most other objects must be tapped to activate them. The game has no indication of this unique property.
- Originally, using a reserve item would have spawned it at the top-center of the screen, requiring the player to tap it again as it fell down.
- Tapping certain amiibo would have spawned a Super Star in an empty reserve. The Super Star allows the player to drag over enemies of any species to instantly defeat them. The POW Block is more powerful as it works automatically, and is less common seeing as it never appears naturally. The dev team didn't want to make some amiibo more useful than others. In the final game, all amiibo provide a POW Block.