Ten episodes form the middle arc of the series, and while an ambiguous ending to the arc seems to render it superfluous to the overall story of Revolutionary Girl Utena, I personally find the themes and the character development in these episodes to be the strongest in the series.
A teacher named Mikage wants to kill Anthy and then make a terminally ill boy, Mamiya, into the Rose Bride in her place - the powers of the Rose Bride presumably allowing him to survive, though Mikage's motivation is less important than the means he uses to achieve his ends.
Mikage has black roses and black rings, dark mirrors of the roses and rings of the Student Council duelists, with which he can control victims into acting as duelists on his behalf. Mikage's first victim is the fiance of Anthy's brother Akio, newly introduced to the series at this point.
The rest of Mikage's victims - none of whom manage to defeat Utena, of course - are all minor characters from the first story arc, now fleshed out and given backstories, motivations, and development of their own. At the same time their storylines also see development for the main characters whom they have a connection to.
Kozue is Miki's twin sister and their story is now shown from her point of view, with her living in the shadow of Miki's piano genius being the cause of her drifting apart. She hates Anthy for now being the object of her brother's attention, so is easily manipulated into becoming Mikage's agent. Further, because of her connection with her brother, she is able to draw a sword from Miki just as Utena draws the Sword Of Dios from Anthy. Not that this helps her to win though.
Shiori is the other girl in Jury's love triangle. Having been in the shadow of Jury's accomplishments for her entire life, she stole a boy from Jury just to get back at her, not realising it wasn't the boy that Jury wanted, it was her.
It was about this point that the pattern became clear to me, that just as the Student Council duelists were the overachievers, the 'beautiful people' as we used to call them at my school, the Black Rose duelists are drawn from the ranks of the ordinary mortals, the supporting cast in more ways than one. This is made even more obvious when you consider who the rest of the Black Rose duelists are.
Tsuwabuki is a boy, noticeably younger than any of the other regular cast members, who is devoted to Nanami and has previously been seen in the humourous sub-plots about Nanami (who has functioned as comic relief throughout much of the series). His attempts to win her attention, no matter how hard he tries, are futile and he ends up as a Black Rose duelist wielding swords drawn from Nanami's heart.
Wakaba is Utena's 'ordinary girl' friend, who is sucked into becoming a Black Rose duelist because of her unrequited crush on Saionji (which was almost directly responsible for Utena becoming involved in the duels back in the very first episode). Saionji was expelled from the school after his last duel against Utena, and ever since then Wakaba has been secretly sheltering him since he, apparently, has nowhere else to go.
I find Wakaba's storyline to be particularly tragic because of the desperate importance she places on being near Saionji (who would never, ever see her in the way she wants him to), and how easily manipulated she is as a result of that.
The last of Mikage's pawns is a character who, unless I was not paying enough attention, isn't even named on-screen until now. Keiko is one of Nanami's three minions; the girls who make up her clique and follow her around basking in the reflected glory Nanami possesses because she is sister of the student president. Her desire to get close to Touga ultimately leads her to become a Black Rose duelist, drawing a sword from his heart.
Mikage is by now out of pawns and out of time - Utena, though it has taken her a while, finds out he is behind the Black Rose duelists and challenges him to a duel. But when Mikage is defeated it seems that all his work is undone in such a way that it is as if it never happened; the 'Mikage Seminar' building where he was based becomes a burnt out shell - and apparently has been all along.
I have a particular dislike for the overused trope of 'it was all a dream,' but Revolutionary Girl Utena cheatily subverts this by only undoing the events - while all the character and relationship developments of this arc remain. The result of this is that "The Black Rose Saga" is not an inessential part of the series, for all that Mikage and his Black Rose duelists are never directly referred to again.
Furthermore, in the background of these episodes, events have been taking place that are of paramount significance to the rest of the story - the introduction of Akio, the gradual building of his part, and the relationship between him and Anthy. This begins with the subtle (or at least I found it so) suggestion of incest, and goes on to the revelation that they have, together, been manipulating Mikage from the beginning.
The (partial) undoing of the Black Rose events serves to hint at some of the weirdness that is to follow in the remaining episodes of the series, almost breaking the viewer in gently for what is still to come.