Cosmic Ark is set in the Alpha Ro star system, which has gone supernova. The player controls two Atlantean space craft in a mission to save two of every alien on each world in the system, in a futuristic Noah's Ark scenario. The larger Ark is controlled between planets, while the "shuttleship" is controlled within planets.
Cosmic Ark consists of two stages, which repeat until the player runs out of lives:
The Cosmic Ark must shoot down meteors while traveling between planets. In order to destroy the meteors coming in each of four directions, the player must move the joystick toward the meteor. Unlike most Atari 2600 games, the fire button is not used to shoot. As the stage progresses, meteors come progressively faster. Once the danger is averted, the second stage begins.
A shuttleship emerges from the Ark during the Shuttleship Rescue stage. Each planet has two "beasties" to beam up to the Shuttleship within a limited time period, and return to the Ark. On either edge of the screen, there are laser turrets that move up and down, firing a beam across the whole screen hoping to blow the ship out of the sky. Meanwhile, occasional meteor warnings sound; If the player can't get return the shuttleship back in time to fire the anti-meteor laser, then the mothership will be destroyed. Saving beasties is not critical to proceeding, although protecting the mothership and shuttleship are.
Each planet to planet trip, a greater number of meteors are hurled at the mothership, and at greater speeds, requiring increasingly fast reflexes. On subsequent planetary visits the laser turrets move faster and fire with greater frequency. Coupled with diminishing time to extract life due to incoming meteorites, makes it more difficult to get even one life form off of a planet.
A player proceeds until there is no more fuel to do so. Each time the Ark is hit, either in space or on a planet, your fuel goes down. The fuel gauge starts at 40, but once it's depleted to 0 the player is on the final ship. A single hit will end the game. Extract life from planets is the sole way to collect more fuel.
This, like most early games, has no end as long as the player survives. The objective is getting the highest score, or making it to the most planets. When the mother ship is destroyed, though, as in the game Atlantis, the mini-saucer is seen escaping. The game Atlantis is considered to be Cosmic Ark's predecessor, suggesting that the Ark is the source of further adventures of those Atlanteans who managed to escape the doomed underwater city. The instructions of Cosmic Ark even refer to the crew as being Atlanteans.