- Donatello (Rob Paulsen) (Debut)
- Leonardo (Jason Biggs) (Debut)
- Michelangelo (Greg Cipes) (Debut)
- Raphael (Sean Astin) (Debut)
- Splinter/Tengu (Hoon Lee) (Debut)
The story begins with Master Splinter narrating a flashback. Before he could become a true ninja, he had to prove himself to the warrior spirit Sojobo by defeating a creature called the Tengu. Cutting to the present, Splinter's voice-over narration continues as he introduces his four sons in the midst of training; Leonardo, Raphael, Donatello and Michelangelo. Splinter then wonders if he has trained them enough as a masked figure appears behind him.
Meanwhile, Leonardo gives his brothers orders for their next training exercise in an obstacle course. Raphael thinks his plan is too complicated and cuts down one of the sandbags, which nearly hits Donatello and Michelangelo. Leonardo scolds Raphael for this and the two begin arguing. Suddenly, the same masked figure that was with Splinter appears in the room. Thinking the stranger has harmed their master, the Turtles attack but are all quickly knocked unconscious.
The second chapter focuses on Leonardo. It begins with a flashback of him meditating with Splinter. Leonardo tells Splinter he is frustrated with his brothers questioning his leadership and compares his situation to an episode of Space Heroes. Splinter tells him he is trying too hard to be like Captain Ryan and that he will only become a great leader if he learns to listen to his brothers and his own instincts.
Cutting to the present, the four Turtles wake up in cages. A voice in the dark introduces himself as the Tengu. He says he has been watching the Turtles for a long time and that the only way they can call themselves "ninjas" is if they pass his challenges. Donatello, Michelangelo and Raphael each try to break out of their cages, but Leonardo meditates instead. Leo realizes that, it the Tengu has been watching them so long, he would know how they would react to being locked up and put them in cages they can't escape from. Then Leo asks if anyone has bothered to check if the cages are even locked. Sure enough, they are all unlocked, but before the Turtles can leave, trapdoors open under each of them and they fall through to parts unknown.
This chapter focuses on Donatello. He finds himself trapped in a room with a tunnel built high in the wall. Then, part of the floor collapses leaving a gaping hole between him and his only exit. Donnie sits down to think and remembers back to a wall climbing training exercise with his brothers. They all climb to the top successfully except for him. Splinter tells him he doesn't have to climb the wall to reach the top, and Donnie uses his staff to pole-vault himself to the top.
Donnie decides to use the same strategy to reach the tunnel. Using the naginata blade in his staff, he throws it and it sticks to the wall beside the tunnel. He then leaps across the chasm, catches himself on the staff, and swings up into the tunnel. As he leaves, the Tengu is watching him.
This chapter focuses on Raphael. His challenge was to control his anger. It begins with a flashback of Raphael punching a punching bag in pure rage, which was because of Leonardo. The chapter ends with Raphael redirecting his anger in a productive way and removes the bridge that the Tengu was on, only to have him hold on to the edge.
This chapter focuses on Michelangelo. Mikey lands in a room that has a single door with an electronic lock. He tries to smash the lock with his nunchaku. Unfortunately it doesn't work, and what's worse, the ceiling starts to crumble. He tries to think about what Splinter had taught him, but he only remembers Splinter telling him to focus on what he has learned.
Panicking, he starts to think of what Donatello would do if he were there. He then remembers a lecture that Donatello gave him about how by-pass electronic locks (Much of which of comes across as "Blah blah blah"). However he's able to focus enough to realize that Donatello told him to pay attention to buttons that looked worn or smudged, because they would give him an idea of what the pass code is. The first and last numbers would contain the most wear. Mikey figures out the code and is out the door before the ceiling crushes him to death.
In this chapter, the Turtles are reunited and face off against the Tengu.
- In Donnie's chapter, when he looks down the deep hole in the floor, a barrel labeled "TCRI" can be seen at the bottom.
- In Raph's chapter, the graffiti tag he calls lame says "Jones is everywhere!" and has the face of a goalie mask.
- In Mikey's chapter, the metal thing he trips on and assumes is one of Donnie's 'toys' is part of a Mousers' head however the mouser head looks different than the one in the show.
- In Issue #1, the Turtles see Master Splinter's staff broken on the floor, but unlike in the original series, the staff appears to be wooden.
- When Donnie releases the retractable blade in his bo staff, it resembles the blade of a Yari (Straight Edge spear) instead of a Naginata (curved edged spear).