In Crisis in Mega City, players experience being the hero and move through over 50 levels of gameplay.
With Captain Atomic missing, the mayor of Mega City plans to name a new city champion, Mookie can't stand it, he is sure that Atomic Puppet will get the glory if he doesn't do anything to stop it, He anonymously invites a few villains to Mega City in hopes that they destroy Atomic Puppet.
Can Atomic Puppet defend the city from these villains while rescuing its people or will Mookie steal his fame and be named Mega City's Champion.
The player plays as Joey and AP as they needed players to control them to launch an attack on enemies of any type, as the player moves the cursor on the screen, they have to click it upon the selected enemy to strike on as they will earn points, and also players are recommended to collect the letters that spell as "ATOMIC PUPPET" in order to gain Atomic Power and another one has a Atomic Puppet Logo, which is called ATOMIC STRENGTH as it is used on charging against the emeny.
On the menu, the player can either go to PLAY or DAILY CHALLENGE, or View Card Page where the player can view on how much it is collected throughout the Play mode.
In the Play mode, the player is able to rescue citizens who are captured by emenies, if the player doesn't rescue in time, either the emeny or Mookie will capture them.
Also if the player gets hits a several times, the player has a small amount of time to click on AP in order to return the battle or otherwise if they don't do it, the player loses as they can hear Mookie's evil laugh.