As Riff Raff and his newly acquired gang is being pursued by the prison guards, Shoeshine Boy is finally able to change into Underdog and fly to the prison. At the shore of the river, Riff reveals to his gang that he has all the components of the Ghost Ship of Captain Kidd. They begin to start rebuilding the ship. When asked why the disguised little guy isn't helping, Riff responds, 'Just in Case'. Just as Underdog arrives at the bank of the river, Riff and the gang set sail, but Underdog cannot see them in the Ghost Ship. After escaping, Riff goes on a crime spree robbing all ships on the sea. Underdog cannot find them since they are invisible. To assist Underdog, Polly hides in a crate on board a merchant ship so that when Riff robs the ship, she can call for Underdog.

The prison warden's chief officer informs him that Riff Raff is assembling a gang and is planning on escaping. They feel that they need to tell Underdog, so they send for Sweet Polly to call for him. When Polly arrives, the chief officer explains what was overheard in the prison from some of the prisoners that Riff has obtained as part of his gang. Polly then calls for Underdog, who, disguised as shoeshine boy, is stalled waiting for a woman to exit the phone booth he needs to change in. Upon hearing that Underdog has been called, Riff makes the decision that his newly formed gang needs to leave immediately, taking with them a disguised little fella. When the gang asks why he needs to be taken along, Riff responds, 'Just in Case.'

Cad, Simon Bar Sinister's henchman, replaces real phone booths with Phoney Booths. When he returns to the lab to tell his boss all the booths have been replaced, he asks what they do. Simon demonstrates by deceiving the milkman that his office wants him to call and directs the unsuspecting milkman into one of the Phoney Booths. The booth jumps and spins and when it opens, the milkman emerges in a trance repeating 'I will do what Simon says'. Simon instructs the milkman to destroy all his milk bottles, then remotely tells him to drive his milk truck into a pole. Then he tells him to go home and await further orders.

Simon toys with Underdog who is now in his power after stepping into one of Simon's Phoney Booths. He makes him dance, bring the 1st National bank to him, and then has him retrieve the Empire State Building. Meanwhile, O.J. Squeeze, Sweet Polly's boss, informs her that Underdog is in Simon's power. Polly takes it upon herself to go out with an axe and destroy the booths. When Simon catches wind of this, he sends Underdog out to destroy Sweet Polly. Underdog arrives at Polly's location and she is trapped.

Simon instructs an entranced Underdog to destroy Polly. As he approaches the trapped reporter, his brain fights the mind control Simon has and finally shatters the bulb above his head breaking free of the mind control. Polly informs Underdog that Simon is behind the Phoney Booths. They head out to Simon's lab to stop him. Seeing them approach, Simon instructs the colonel he has in his power to shoot Underdog down. Underdog puts Polly down to fight the army. One of the projectiles Underdog deflects, lands on the colonel's trance bulb above his head and frees him of Simon's power. Underdog takes several projectiles and blows up Simon's lab and sends a fleeing Simon and Cad hurling into the air landing in a tree.

At first it look like Overcat is going to win. But even though he's as strong as Underdog, he's not fast. Underdog uses his speed to beat Overcat. When the cats kick Overcat out of Felina, Underdog gives them coconut trees so they never run out of milk.

Riff and his gang decide to rob one more vessel before they go for their biggest catch, The Queen May. But, Polly has hidden herself as a decoy so that she can call for Underdog once she is on board the Ghost Ship. When the gang opens the contents of the merchant ship they just robbed, Polly emerges and runs calling for Underdog. They capture her but the gang is fearful that her cries will bring Underdog. At this point, Riff finally reveals what 'Just in Case' is,...Just in Case Underdog comes! The disguised fella is really a witch doctor who, along with a voodoo doll in the form of Underdog, is able to manipulate our hero and leave him helpless

Polly watches helplessly as Underdog fall victim to the witch doctor's voodoo spell. Luckily, a passing sea gull grabs the Underdog doll and takes it to a remote island. There, a monkey takes the doll to the top of a volcano, preparing to throw the doll in. In the meantime, Riff Raff And his Ghost Ship Gang sneak aboard the Queen May and begin to loot the ship. Needing every ounce of his super strength to break the witch doctor's spell, Underdog takes one of his super energy pills. Free of the spell, Underdog flies to the Queen May with a paintbrush and a bucket of paint. Before long, the ghost ship is reveled by the superhero-cum-artist. Riff Raff and his Ghost Ship Gang are captured, and returned to prison.

After all the reporters and news crew leave the site of the strange object, two stonehead creatures from the planet Granite, named Gravel and Crusher, emerge from the craft with their Granite Gun. Their mission is to collect 10 slaves to bring back to their planet to work in the rock mines. After reporting in to their fearless leader, Captain Marblehead, the two buffet on some of Earth's stones and marble. They then proceed with their mission and collect 10 slaves, which so happen, include Shoeshine Boy and Sweet Polly. Before they leave for home, they are observed and the army tries to stop them.

Just before they are ready to head home with their slaves they captured with the Granite Gun, Crusher and Gravel are confronted by the army. Using the Granite Gun, the stoneheads defeat the army and head for Planet Granite. They then present the slaves to Captain Marblehead who orders them cracked open from their stone enclosures. He explains that they were brought to mine the rocks for the food for the Marbleheads and orders them sent to the mines. While working in the mine, Polly tries to call for Underdog, but with him disguised in his Shoeshine Boy persona, he has no place to change. He then suggests a revolt and the group makes a plan.

In this final episode, Shoeshine asks for a drink of water after being placed in his cell. When he gets it from the guard he tosses it into the guards eyes. While the guard tries to regain his sight, the prisoners escape locking him in the cell. The next phase of their plan is to get the Granite Gun which is in the throne room of Captain Marblehead who is enjoying his meal. Polly attempts to clobber the Captain with a pipe, but it has no effect on his stone head. He then calls for the guards who round up the prisoners. In the confusion, the guards hurl a projectile at the prisoners who duck and allows it to break open a wall to reveal a phone booth. Shoeshine sees this opportunity and changes into Underdog. He races to free the prisoners only to face Captain Marblehead and the Granite Gun. Underdog gets temporarily made of stone but then breaks free. He then melts the Granite Gun with his x-ray vision. After defeating Captain Marblehead, he tells him to mine his own rocks in the quarry and then heads home and frees all those who were turned to stone.

After a violent thunderstorm ravages the city, the community gathers in front of one of the steel buildings to see a message revealed inscribed on its side: 'To Underdog, A Rhyme in Time Saves Nine'. Sweet Polly asks Flim Flannigan at the police station what it means. Flim explains it could only be the work of Slippery Eel. A few weeks earlier, Eel, Fish, and their henchmen attempted to rob an armored car. They were caught by Underdog and were sent to the maximum prison with the electric fence. Still determined to get out, Slippery Eel tells his boys that he is going to climb the fence now that the power didn't seem to be on. Midway climbing the fence, the guards see him trying to escape and turn on the electricity. However, instead of electrocuting him, it electrifies him, and he then claims that he is now 'The Electric Eel'. He shoots bursts of electricity at the fence and wall and escapes with Fish and the gang, all the while vowing to get even with Underdog.

Flim and Polly agree that humble, loveable Shoeshine boy would be able to make sense of the riddle 'A Rhyme in Time Saves Nine'. Shoeshine deduces that 'rhyme' refers to Underdog, since he always talks in rhyme, 'time' refers to clock, Polly suggests Big Ben, but says that that's in London. Shoeshine deduces, what the biggest 'Ben' is around in the city, to which Polly responds 'Ben's Jewelry Store' (not Big Ben). As for 'Nine' Shoeshine deciphers that there are nine players on a baseball team and baseball is played on a diamond. Polly then sums up the solution of the riddle that if Underdog gets to Ben's Jewelry Store he can save the diamonds. She then tells Shoeshine to hurry and find Underdog. Shoeshine immediately rushes to the nearest phone booth and becomes Underdog (no waiting) Prior to arriving the Electric Eel demonstrates to Ben and the others he is holding up, the trap of an electrical field he has waiting for Underdog. When Underdog arrives, he steps into the trap and can't break free of the electrical field.

The Electric Eel traps Underdog in his electric cage. As the cage closes in around him, the cage fills Underdog's body with thousands of volts. Before he dies, Underdog asks the villains not to throw him into the city's lake. Underdog's body is soon limp at the bottom of the electric cage. Sensing victory over his foe, the Electric Eel takes Underdog's body to the city lake and throws it in. Free from Underdog, Electric Eel begins his massive crime wave across the city. Still not satisfied, the Eel decides to commit the ultimate crime.

The Electric Eel and his gang head for Washington, D.C. to take over the country. But Underdog is on the mend; the waters of the lake sap the electric charges from the Eel's trap. Underdog heads for Polly's TV station, where he finds out that the crooks are heading for our nation's capitol to force the President to turn over control of the country to them. Quickly, Underdog heads for the Sandwich Glass Blowing Factory. When he gets there, he asks the factory's owners to show him their biggest glass jar. When they can't find a glass jar big enough to hold a man, Underdog learns how to blow his own giant glass jar. Armed with the jar, Underdog flies to Washington, D.C. where he puts the Electric Eel in the giant glass jar. One less Electric Eel on the streets.

Simon Bar Sinister makes a vacuum gun which he uses to catch Riff Raff, Electric Eel, Batty man and all of their men for his army while Underdog is saving a sinking ship.

Sweet Polly is captured by Simon and calls for Underdog. Unfortunately, his energy was drained from saving the ship so he and Polly were sucked in the vacuum gun and Simon starts to fill it with water.

Underdog's ring has fallen off his finger; Polly dives underwater to find it. Meanwhile, Simon and his army are using their vacuum guns to steal all the money in the US.

Polly finds Underdog's ring. He takes his energy pill then defeats Electric Eel, Riff Raff and Batty Man. Simon uses his vacuum gun but since Underdog has his powerful strength back, this time it doesn't work. Using his atomic breath, Underdog beats Simon and Cad and returns all the money.

Simon has finally forced the people of the city and the world to give him ultimate power. Underdog is still stuck in the polluted mud of what was once the Atlantic Ocean. He swallows a super energy pill from his ring and, regaining his super powers, he flies back to the city and tricks the two villains into giving him all of Simon's jars of water. In retaliation, Simon prepares to destroy the Big Dipper with his pistol. Our hero takes the gun away from Simon and knocks the two villains out. Underdog refills the world's entire waterway, saving the world once again.

More unsuspecting people fall prey to Simon's Phoney Booths. A banker steps into a booth and is ordered to bring all the money from the bank. An engineer steps into a booth and is ordered to bring his train to Simon's lab. A colonel steps into the booth and is ordered to bring the army to Simon Bar Sinister's house. On a college campus, students try to see how many they can fit into a booth, but of course, it's a Phoney Booth. Each emerging student is told to do a task. News finally gets to Shoeshine Boy who steps into a booth to become Underdog, but, it is a Phoney Booth.

Polly tells Overcat about Underdog but he is not worried; he kidnaps her to milk the cows. Polly calls for Underdog. When he gets to Overcat's planet, he is placed in a rubber ball trap that drains his energy. He is taken to help Polly milk the cows.

Polly gives Underdog his energy pill and he beats Overcat's men. Next, Underdog takes Polly and the cows back to earth. Overcat challenges Underdog to a fight for the cows. If Underdog refuses, Overcat will attack Earth.

The planet Felina's milk wells have run dry which makes the evil ruler Overcat mad. He and his men go to Earth and steal all the cows. However, they don't know how to get the milk from them so they grab someone who does... Sweet Polly!

A strange object crash-lands on earth. A group of scientists check out the mysterious object, determining that it's a harmless, dead comet. The scientists leave the scene unaware of the fact that a secret door opens from the center of this strange thing and two evil looking space aliens emerge from this strange object.