The famed first issue! Where it all began... The book opens with the Turtles battling about 15 thugs in an alleyway, and winning. When the police show up, they head home to the sewer. The tell Master Splinter of their victory, and Splinter decrees that they are now ready to be told of their mission, a mission of revenge! Splinter, for the first time, tells the Turtles their origin:

Splinter was once the pet rat of Hamato Yoshi, the greatest shadow warrior of his clan, known as the Foot. Mimicking his Master as he practiced, Splinter eventually became as adept as Yoshi. Yoshi also had a bitter enemy, a fellow clan member, Oruku Nagi. They competed in all things, but none greater than for the love of a beautiful girl, Tang Shen. They both fell in love with her, but she only loved one of them in return: Splinter's master, Yoshi.

Oruku Nagi became extremely jealous and one night he, in a fit of rage, went to Tang Shen's home and demanded that the girl love only him. She refused, and Nagi beat her. Just then, Yoshi arrived, and after seeing what Nagi was doing to his beloved Shen, flew into fit of rage and killed Nagi. This was a shameful act in the eyes of the honorable Foot Clan, because one member must never kill another. Because of this, Yoshi had two choices: he could take his own life in ritual suicide and hope for honor in the next life, or he could flee the Clan and start a new life. Yoshi chose the latter, and fled to New York City with Tang Shen, Splinter, and a few meager possessions. He started his own martial art dojo and all went well for years.

Back in Japan, Nagi brother, Oruku Saki, had sworn vengeance against Yoshi, the man who had killed his beloved sibling. His intense anger pushed him to become a premiere ninja in the Foot Clan, and as a reward, the Clan sent him to New York City to lead the city's branch of ninjas. Saki saw this as his opportunity to reap his revenge against Hamato Yoshi and slay him. Saki build the New York branch of the Foot into a criminal ring involved in many crimes; from drug smuggling to their specialty-- assassination. Saki never forgot his goal, though. After a while, he tracked down Hamato Yoshi and Tang Shen down, and while Yoshi was away at work, Saki broke into his apartment and murdered Tang Shen. Saki then waited until Yoshi returned home. As Yoshi entered his home he saw his dead wife on the ground and her murderer: Oruku Saki, who proclaimed to be "the Shredder". Saki and Yoshi fought, and during the struggle, Splinter's cage was broken, freeing him. Eventually, the youthful Shredder got the better of older Yoshi, and he was slain as well. Splinter, anguished over the death of his family, fled to the alleys and lived off of garbage scraps.

But then, one day, a TCRI truck drove by, and a canister flew out of the hold. The container struck a man in the head, bounced on the pavement, and smashed into a young boy's aquarium filled with baby turtles. The shattered aquarium, canister, and turtles all fell into an open manhole cover, dropping them into the sewers. The canister held some strange chemical,and it smashed when it hit the sewer floor, covering the small turtles with the strange glowing ooze. Splinter went to see what had happened to the turtles, and seeing them covered with ooze, he picked them up, cleaned them up as best he could, and gathered them up in an old coffee can. He took them with him, and in the morning, the wise old rat received a shock: the Turtles had doubled in size, becoming more human-like as he watched! He then realized he, too, was growing. Eventually the turtles spoke, and Splinter began to plan his own act of revenge. He began training the turtles in the art of ninjitsu that he had learned from Hamato Yoshi. He named each turtle after a Renaissance artist, whose names he had found in an abandoned book.

After hearing their origin, the Turtles know what must be done. They had to avenge the death of Hamato Yoshi. They had to defeat the Shredder in combat. Raphael goes on a mission to deliver a message to Saki, which demands that Saki meet the Turtles on the rooftops to fight to the death. Shredder brings a ton of Foot with him, and a battle erupts between the Turtles and the ninjas. The Turtles win hands down, forcing Shredder into combat. The Turtles use their teamwork to beat Saki. After defeating him, they demand he commit ritual suicide to regain honor he lost when he murdered Yoshi and Tang Shen. He refuses and takes out a grenade, saying that if he must die, he will take the Turtles with him. Don saves the day by launching his bo staff into Shredder's jaw, which knocks him and the grenade from the rooftop. As Shredder falls, the Turtles go to the edge of the roof, seeing the grenade go off in a blinding flash. The Turtles breathe a sigh of relief. They have preformed the task that Master Splinter had trained them for... or have they?

This issue, which introduced April O'Neil and Baxter Stockman to the TMNT universe, begins with the Turtles and Splinter watching the news. The reporter is doing a story about Dr. Baxter Stockman and his new invention: the Mouser, a rodent-killing robot. Stockman, with the help of his lovely assistant April O'Neil, shows the Mouser's ability to track and slay rats. Splinter tells the Turtles to be careful with this new threat in the city.

Several weeks pass, and in that time, many bank robberies have occurred. April reads the paper to Stockman, which describes small tunnels dug into the bank's vaults. April says that the Mousers would be able to do this, which Stockman dismisses, stating that April had helped program them, and that she should know better. He then takes April to an underground security level of the lab where an army of Mousers are being built. April demands to know where he got the funding to build hundred of Mousers, when she concluded that her original suspicions were correct: the Mousers, controlled by Stockman, were robbing the banks! Stockman then reveals his plan to blackmail the City. April is majorly confused now, as she notes that Stockman could have made millions legally with the Mousers. Stockman replies that he's not doing it for the money--that's just an incidental, a by product--but because it's fun! April realizes that Stockman is quite insane, and she bolts for the door. Stockman programs the elevator to drop her into the sewers, and sends several Mousers to kill her.

Just as she's about to be mauled, our favorite green heroes show up and they destroy the robots. And just like every single re-telling of how April met the Turtles, April faints. The Turtles take April to their sewer lair, and when she finally wakes up, they tell her their origin. The Turtles then turn on the news and hear Stockman making his demands of the City. He had the Mousers dig tunnels underneath every corporate headquarters in New York, and if a ransom is not paid for each building, he'll have the Mousers destroy the buildings' foundations, which will cause them to crash.

The Turtles and April sneak into the building, deciding that it's up to them to stop the mad Stockman. They confront him, and he sets off an explosion and traps them in the lab. The Turtles manage to blast a hole in the wall, but that leads to a storage room full of Mousers. The army of robots attack, and Leo, Raph, and Mike try to hold them off, but there are too many! Just as it looks like curtains for the five, Don and April manage to program the computer to shut down all power in the lab, including the Mousers.

In this issue, the Turtles return to their sewer home to find the Master Splinter has been kidnapped by the Mousers. They call the only person that can help, which happens to be April O'Neil. She shows up in her van, and they get in involved in a wild car chase when the police mistake Aril's van for a getaway van in a recent robbery. After the Turtles and April try to lose the cars that were tailing them, they pull up next to a van which is identical to April's. While the police try to figure out which van is holding the criminals, the Turtles and April make their escape. They head for her apartment to rest and make plans ro find Splinter. The Turtles conk out in the living room,

Meanwhile, Splinter is injured while battling the Mousers in the sewer.Just as the killing machine are about to make minced meat out of Splinter, they turn around and march in the other direction. Dazed and nearly unconscious, Splinter escapes by crawling through the sewer system. He's discovered by two human guards who take him to the TCRI laboratories. Inside, Splinter discovers that the humans that work there are actually small alien creatures that resemble brains, and they use robotic bodies to disguise themselves.

Note: These aliens are the precursors to what will become Krang in the cartoon.

The Turtles are exercising on the rooftops of New York City when some members of the Foot Clan show up and attack our heroes. The Turtles whip the ninjas, but Michaelangelo receives a serious cut on his arm. The ninjas beaten, Raphael notices that the building directly beneath them has the TCRI logo on it. The Turtles, being thoroughly freaked out by finding the place that created the ooze that mutated them, decide to investigate. But before they can, they head to April's to patch Michaelangelo up.

Once everyone's rested up, they head back to the TCRI building. Donatello defeats their security cameras using a clever plan, and they make their way to the building. They sneak around for a while and then stumble into a bizarre techno lab. Master Splinter is being held in suspended animation in some sort of tube, and Raphael prepares to shatter the tube. The Utroms suddenly arrive in their robotic bodies with stun-guns. A fight breaks out, but it ends when the Turtles get in the middle of a strange device that the Utroms won't fire at. Mikey attempts to vault over the aliens' heads to find a way to escape, but his recent injury cause him to fall. He crushes a control panel, causing the machine the Turtles are standing on to activate! Mike is grabbed by an android as the device energizes. As the other Turtles are enveloped in cosmic rays, Michaelangelo frees himself, runs, and dives into the machine to be with his brothers, wherever they may be going!