While First Pixel Shooter features no main character, the game begins with and mostly follows Pvt Johnson, codenamed 'Doodles'. The game starts with Doodles completing recruitment training, in which mid way through the Red Army attacks the training base. Afterwards, Doodles, accompanied by Blue
Army reinforcements captures enemy documents in the Bloxville city square, which outlined enemy weaponry. In preparation, he is sent to a secret Red Army base to investigate whether the Red Army really has nuclear capabilities. Doodles confirms this, and escapes the base. Doodles is then sent on one last mission before a reprieve, where he and Pvt Crunchy must capture outposts in the Somar Desert. While en route back to base, their helicopter gets shot down.
Afterwards, the player assumes the role of Corporal Cricket, a soldier of the Red army. Cricket and Pvt Goose make their way out of a city within the Somar Desert network, eventually finding a boat which they take down the river. After fighting off Blue helicraft, they reach a cave where they find Doodles who had washed ashore and taken shelter within. The Red Army segment ends with a narrative from Pvt Crunchy, who somehow makes his way back to the Blue's HQ. He meets with Srg Mcpickle, who leads on to suspect that Crunchy knows what is going on internally with the Blue Army, and kills him.
Narration than jumps to Lt. Jackal, a hardened soldier of the Blue Army. He is sent to the Tatawn Jungle to save codename Weasel, a Purple saboteur. Although not with the Blues or the Blue Army, in return of being rescued, Weasel agrees to aid in the war effort. After a flashback to Jackal's past battles, Weasel and him go to the Tophe Tundra, where a Red base in the north lies. There Weasel destroys enemy weapon arsenels. When they split up, Jackal is then captured.
The final missions of the game begin with Pvt Milkshake, who must defend two soldiers defusing a bomb in the streets of Malefor. He is then sent to infiltrate the city hall, which was locked down by Reds, where he discovers the whereabouts of Lt Jackal. They send Milkshake to the prison to rescue him.
Doodles, piloting a sub from a Red sub pen breaks into an enemy base to acquire helicraft to make it back to HQ. Before he does, he is confronted by Pvt Cricket, who quickly recognizes and threatens him for killing his men. Doodles reports to HQ and is sent on one final mission, accompanied by Cricket who believes they should work together, and tells Doodles he has been expended for the war effort, and his hands are too stained. Tired of fighting, they attempt to initiate a truce. While advancing through the city of Azol, they meet up with their contact, who is guarding Green hostages. Doodles' final mission is to execute the hostages, to 'send a message' to the other armies. Doodles relcutantly obeys, but shortly after, the city is nuked from a mystery source. What happens afterwards is unknown.
The last three missions begin with Jackal, who makes his way through a Red transport ship, which carries the leader of their army. Jackal locates his target, but is told to seize fire due to the ship docking soon. Milkshake then must fulfill the last request of the Blue Army, and that is to finish Jackal's mission - to kill the Red Army leader. Above the ocean, atop the freeway lies the last stand of Red enemies, leading to a helicopter carrying the leader. Milkshake takes him out, and is declared a war hero. The game ends with the other armies withdrawing from and ending the war.
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