The story of Nanostray is fittingly simple for a shoot 'em up. The protagonist has recently awoken inside of his ship, the SHN-2K5, having lost all memories. He finds that a location is still programmed into his ship's console, and chooses to proceed to his destination while combating enemy ships.
At its core, Nanostray's gameplay matches that of the typical shoot 'em up. The player is in control of a small ship with a disproportionately massive amount of firepower. This ship must be guided through waves of enemies, with each level culminating in a boss encounter.
The player may switch between four separate weapon types on the fly through use of the touch screen. Each of these weapons has its own secondary, more powerful method of firing. These secondary weapons share an energy bar that may be replenished by collecting blue coins.
- Pulse: The pulse is the main weapon of the SHN-2K5. It is a simple weapon that fires rapidly forward in bursts of three, delivering a great deal of firepower with no frills.
Pulse Sub-weapon: The sub-weapon of the pulse is a solid beam that fires directly forward. Like the pulse itself, it is an efficient damage-dealing weapon, and will serve effectively in most situations.
- Side-shot: The side-shot fires bursts of three out of each side of the SHN-2K5. The weapon is practical in relatively few situations, as enemies rarely approach from the sides. It can, however, be useful against more mobile bosses.
Side-shot Sub-weapon: The sub-weapon of the side-shot is a powered up version of the main side- shot, firing more rapidly and in a narrower range.
- Seeker: The seeker fires out lasers that will curve toward enemies when fired. While it has lower firepower than the other main weapons, the seeker is useful when smaller numbers of enemy ships emerge in complicated patterns, as less maneuvering is required to hit the target when using this weapon.
Seeker Sub-weapon: The sub-weapon of the seeker is a single, large burst of energy that homes in on and deals a great deal of damage to a single target.
- Lightning: Lightning is a beam of electricity that fires out directly in front of the ship. Once it hits a target, however, it will lock onto the target until it is either destroyed, obscured, or until the player releases the firing button. This weapon is best used against bosses, as the SHN-2K5 may simply lock onto the boss's weak point, and then focus entirely on dodging attacks.
Lightning Sub-weapon: The sub-weapon of lightning is a cluster of electric beams that surrounds the SHN-2K5, dealing a large amount of damage in a circular pattern. This weapon is best used against enemies that attempt to surround the ship.
Two different kinds of coins may be collected as a reward for defeating enemies. Yellow coins are dropped by large enemies, and they reward the player with bonus points. Blue coins, which are dropped when a wave of small enemies is defeated, will refill the sub-weapon's energy bar, grant brief invulnerability, and give points. If the player refrains from using any of the sub-weapon bar between collecting blue coins, a point multiplier begins to form, granting an extra 500 points per coin until a sub-weapon is used, breaking the multiplier. The ship is capable of sucking in coins at the press of a button, but doing so results in a lower score at the end of the level.
Scoring at the end of each level takes into account numerous factors based on the player's performance. These factors are displayed separately at the end of each level, adding up to a "New Score" that represents your total score for the level. This score is accompanied by a letter grade to apply comprehensible value to the score.
- Old Score: A combination of points earned from defeating enemies and points earned from collecting coins.
- Wave Bonus: Each time a full wave is destroyed, the player receives a bonus of 500 points for each ship in the wave. If every wave is destroyed, the player receives the maximum bonus of 10,000 points.
- Valor Bonus: In order to discourage players from constantly firing and attracting coins to the ship, a valor bonus grows for every moment that the player is neither firing a weapon or attracting items.
- Ship Bonus: For each life remaining at the end of a level, the player receives 3,000 points.
- Smart Bomb Bonus: For each remaining Smart bomb at the end of a level, the player receives 3,000 points.
Adventure mode takes the player through several sectors, allowing a choice between a cluster of a few levels at a time, ramping up the resistance level with each new sector. The levels, in order that they are presented, are:
- Mitsurin Jungle: A forested area featuring a great deal of greenery and a large river.
- Mokuzu Depths: A flooded city featuring partially submerged buildings and marshes.
- Sunahara Desert: A sprawling desert with a great deal of cloud cover.
- Hibashira Plains: A volcanic region that is sometimes obscured by steam, smoke, and eruptions.
- Sekihi Belt: An asteroid belt in which some small installations have been constructed.
- Sekai Outpost: A large installation built in the sky.
- Chuuroh City: A bustling city swarming with security ships.
- Zenshoh Station: The player's final destination, Zenshoh Station is an enemy base featuring large, armored ships and aggressive enemy waves.
Arcade mode allows the player to select any level and play through it for a high score. The player may then generate a NanoCODE to share on the game's official website.
Challenge mode provides 22 separate tasks for the player, in which he or she must strive to either earn a high score on a level or complete it with handicaps. Each completed challenge unlocks either a piece of concept art, an enemy model, or a piece of level music.
Nanostray features single-card simultaneous multiplayer, offering multiple competitive game modes. A sudden death variant is offered for each mode, in which death results in an instant loss, regardless of score.
- 120s: Players take on a level for 120 seconds. Whichever player earns more points wins.
- 60s: Identical to 120s, except with a 60 second time limit.
- 25k: Whichever player earns 25,000 points first in the chosen level wins.
- Bonus Race: Enemies drop yellow coins, and the player who collects the most by the end of the level wins.