The bulk of the game is played in an overhead 360-degree shooter style similar to Geometry Wars where movement is performed with the analog nub and shooting takes place in all directions using the ABXY buttons in place of a second analog control. These stages take place with the microscopic ship of series fame flying over giant cells fighting off infections and viruses (bad guys) and picking up DNA sequences. The primary focus of these stages is to eradicate all enemies and to collect all DNA strands. These are referred to as Twin Shooter, or Ground missions. The Nanite ship fires three bullets per shot in this mode, and can utilize one of four secondary weapons with the R button. The spread of the bullets may be modified with the L button.
The second gameplay style comes in the form of 2.5-D boss battles which take place on a large circular area with a boss character in the center. From the perspective on-screen, the player moves the ship left or right along a 2-D plane and must fire into the background at the boss, or to either side against other attackers or pieces of said boss character. The primary focus of this mode is simply to destroy the boss character. These are a variation of the Twin Shooter missions.
The third perspective is that of a 3rd-Person, behind-the-ship view flying through 3-D corridors within an organic body firing on infections and other things. Enemies move and swirl into the play area in typical shmup forms and patterns. Players are tasked with dodging obstacles as well as destroying enemies and this is the only mode where dodging environmental hazards is really important. The primary focus of this mode is survival culminating in a boss battle. These are the 3D Action Shooter, or Flying missions. In this mode, the Nanite ship fires single shots and may use some but not all of the secondary weapons.
Besides the main Story Mode, there is an Arcade Mode wherein stages completed in Story Mode may be replayed for fun, high scores for Leaderboards, and to complete specific challenges set for each stage. Challenges include completing without dying, completing without using the secondary weapon, or obtaining a set high score. Completing challenges earns Nano Coins which are used to purchase songs for the Jukebox or enemy profiles for the Nanopedia. Finally, there is also a Boss Rush Mode unlocked after completing the game, and this mode also allows for earning Nano Coins. Nintendo 3DS Coins may be converted into Nano Coins.
Plot-wise, the focus of the game is similar to the previous entries, in that players assume the role of a nanite vehicle and travel inside an organic body attempting to thwart the deadly Nanostray virus, and to prevent it from spreading throughout civilization. This includes numerous boss battles, both as stand-alone events and as the climaxes of some stages. The levels are broken up into Cell Clusters, and within each Cell Cluster is a number, usually around 5 or 6, individual Cells, which represent the stages. Overall, there are 32 Cell stages and 10 boss battles.
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