Some TMNT stuff really isn't for little kids.
The issue begins at the Foot Clan's genin training facility in Westchester County, New York. The head teacher Toshiro is leading a group in a training session, teaching them the importance of moving in unison. Karai appears and intentionally surprises the group, seeing which students are startled and which are not. She seeks council from Toshiro. Karai tells Toshiro she is unsure of what direction to proceed in; she struggles to accept her new place in the clan (under Leonardo, now a chūnin). She knows she cannot hope to challenge her grandfather Oroku Saki for control of the clan and win, nor can she leave the clan for without it she feels she is nothing.
She tells Toshiro how in her youth her father Oroku Yori told her stories of the Foot Clan's glory and told her to draw strength from the, but saw that it was apparent that he himself did not, having turned the clan into a legion of lawyers and accountants. On one occasion, she saw one of her father's advising subordinates, Nakamura, speak to him with disrespect, and how he brushed it off with the promise of monetary gain. Caught eavesdropping by her mother, she is sent to he library to occupy herself. It is then that she found the Ashi no Himitsu, the book containing all the history and secrets of the Foot Clan. She studied it in secret, learning everything she could. For years she lived a double life: the prim, proper upper class girl her mother wanted her to be by day, and the ninja her father never was by night. One night, Oroku Saki appeared before her in a dream. He compliments her form, good for one with no formal instruction. Saki admires that she does not fear him. Karai says she has nothing to fear from a dream. Saki slashes her across the hand and asks if one feels pain in a dream. She says he is a ghost then, but still shows no fear. She says she plans on bringing the Foot Clan out of the mire her father dragged it into. Saki tells her that they will do it together. He may be dead, but he tells her that she can bring him back to life.
Karai spent the next few years building the clan's resources, recruiting capable bodies to her cause and eliminating those who were responsible for dragging the clan down. Eventually, Karai hunted down Nakamura, the man who she'd witnessed disrespect her father, and killed him. Without him to aid in the running of the clan, her father eventually died of stress.
She laments to Toshiro that after rebuilding the Foot Clan and resurrecting its jōnin, he chose another as his second-in-command. If she has nothing to offer but her past accomplishments, she wonders, what use is she? At that point Leonardo arrives and derides her for coming to whine to an old man, for not having the strength to deal with things on her own. Leonardo says that he was sent to evaluate the effectiveness of the training facility, and he has deemed it nearly worthless. Karai tells him that Toshiro is an excellent teacher but he has not been given enough time to train the new recruits. Leonardo tells Karai that her opinion is worthless, and her only worth to him is in how fast she can do what he tells her to. Leonardo continues provoking her, taunting her with her poor ability to lead. Karai attacks him and Leonardo is pleased, eager to put her in her place. During their fight, Karai realizes that Leonardo's movements are slower, less sure. She knows she could finish him once and for all if she chose to. Karai feigns defeat and Leonardo leaves. Toshiro asks why Karai stayed her hand. She explains that if she had killed him, her grandfather would kill her for disobedience. She knows she must change Oroku Saki's mind about Leonardo first. She vows to have her revenge, and makes the decision to look to the future rather than the past.
Two days later, Karai has gathered potential recruits (two of whom are Bebop and Rocksteady) at Shorai Research & Development, one of the Foot Clan's facilities. She tells them they have all been chosen for their understanding that power is what makes one last in this world. She tells them that there is one final test before making the decision on who will be chosen for the procedure. They will fight until the last two standing.