Ninjas are a constant feature in Usagi Yojimbo's universe. They are pretty much the go-to cannon fodder baddies, along with "brigands", and the three factions we see (Mole - Kagura, Bat - Komori and Cat - Neko) attack Usagi and his allies on a consistent basis.
They have, however, their own internal and external wars, which lead to some interesting stories. All of them are vying Lord Hikiji's favour, who uses them to his advantage, pitting them against each other and making them compete for his approval.
The clan currently on top is the Neko ninja. They were some of Usagi's first adversaries, appearing in his second story, but became temporary allies under the leadership of Shingen during Book 4: "The Dragon Bellow Conspiracy"
. After that, Shingen is replaced by his sister, Chizu, but her position was challenged from the very start, seeing as she is a female ninja (kunoichi
). Even so, she is capable of holding her own and carrying out several errands for Lord Hikiji. But, after her first meeting with Usagi, in "Shades of Green
" (a crossover with the TMNT), she develops a soft spot for the rabbit, which makes it a bit more difficult to accomplish her work.
She is eventually expelled from the Neko ninja and becomes a fugitive. This is the story of her fall from grace.( The first tenet of ninja is deceit )
This story was collected in Book 16: The Shrouded Moon
and Usagi Yojimbo Saga vol. 3
Barring (possibly) Chizu, Usagi constantly expresses his hatred towards ninjas all through the series. Which is funny, given he has starred in all three TMNT cartoon incarnations, has crossed over with them in at least three canon stories and considers Leo one of his best friends.
A running gag is that Chizu always departs leaving Usagi with a kiss, "a way foreigners use to show affection". Maybe that is why he tolerates her.
Next, the most skilled fighter in Usagi's universe: Inazuma, the lightning!