Quick Kick welcomes the trainees to masterpiece bomb theater and explains that Bazooka must disarm the bomb or they will all die. After cutting the yellow and red wire, Bazooka pauses and ponders what colored wire he should cut next. Quick Kick points out that there is only one wire left, but Bazooka cuts it too late and a small sign pops up and has one word: bang. Suddenly, an earthquake begins to rock the island. Bazooka falls into an opening crack in the earth, trees smash huts and large boulders crash down from the mountains. The trainees flip and dive out of the way of the boulders and survive the earthquake.

Tako reports to Quick Kick that everyone survived but Bazooka, and Quick Kick kneels near the crack in the earth and explains that Bazooka was no bomb expert but was a good man, nonetheless. However, a voice within the earth shouts, “Throw some rope!” Bazooka climbs out of the earth and wonders if he should cut the green then red wires first. Quick Kick laughs and tells his friend that he can figure it out later and that they need to travel to the Tokyo base.

Cobra Commander explains to the Baroness that the destruction of the training camp means nothing to him and that the next target is Tokyo, however, he asks the Baroness for some information. Climbing into a FANG helicopter, the Baroness simply says, “Leave that to me.” And she flies away.

Lady Jaye tells Flint that the earthquake at the training base measured as an eight on the Richter scale, but Flint is still confused why an earthquake wreck the area since there are no active faults nearby. Lady Jaye explains that Bazooka thought he explosions before the earthquake, and Flint and Lady Jaye come to the conclusion that since Japanese scientists are trying to prevent earthquake with precisely timed explosions, Cobra may have found a way to create earthquakes.

Lady Jaye and Bazooka drive to a Shinto shrine to meet Japan’s most knowledgeable seismologist, Dr. Morita, and after they remove their shoes and walk inside, two men in blue robes grab Dr. Morita and carry him away. The Joes chase them up an incredibly large number of stairs and then learn that they have chased Storm Shadow and two of his own trainees, who dress like their teacher.

More of Storm Shadow’s students appear and the Joes fight back while Storm Shadow turns his back to the Joes and tells his students that the Joes are not worthy of his efforts. The Joes are pushed over the railings and tumble down into a pond. As the Cobra ninjas rush toward the Joes, a Silver Mirage motorcycle flies toward them and screeches to a halt. Quick Kick arrives and Bazooka, who smashes two Cobra agents’ faces together, tells his teammate that he is late. Explaining rush hour traffic made him late, Quick Kick lands a foot into Storm Shadow’s chest and the two exchange blows, however, Storm Shadow jumps over a wall while noting that Quick Kick’s fault, overconfidence, has allowed him to escape.

Lady Jaye orders Quick Kick and Bazooka to follow Storm Shadow and the two Joes follow him to a Japanese puppet theater. While on a stage, the Joes are attacked by puppets, however, they knock them away and Quick Kick yells that Storm Shadow will have to try harder. But Scrap Iron replies that the Cobra ninja has stepped out and activates a trap door. The Joes fall through the door and land on the ground, and Scarp Iron drops a bomb with a head similar to the puppets and adds that his friend is a dynamite guy.

Telling Bazooka that the Joe will only disarm the bomb over his dead body, Quick Kick directs his friend to a weight and pulley system that lifts them up to the theater’s balcony. They jump out a window and dive into a truck hauling vegetables just as the bomb explodes, demolishing the building. Bazooka emerges from the pile of food and then asks Quick Kick if he would like a banana.

Lady Jaye arrives at Dr. Morita’s house and radios Flint to report that the place is in shambles, however, she has found a map that may help the Joes. But before Lady Jaye can return to the Joes’ base, the Baroness stands at the doorway and tells Lady Jaye that she is not in a lending library and then signals the Cobra ninjas to drop a net onto Lady Jaye, who struggles to get out but is told that the net will only become tighter each time she moves.

Activating the homing beacon in her boot, Lady Jaye’s signal is picked up by Flint, who orders Quick Kick and Bazooka to take Tako on a rescue mission to free Lady Jaye. The three rescuers arrive at the Cobra base on a raft and Bazooka stops to disarm a mine, however, Quick Kick tells his teammate to leave the mine alone. Stuttering in agreement, Bazooka and his teammate continue to rush to Lady Jaye’s rescue. Quick Kick clasps his hands together and helps boost Tako to the top of a wall so that she can latch a hook and a rope to the wall and allow the Joes to climb up.