The series has a somewhat understated yet believable Downer Beginning, with Haruyuki being bullied at school. Worse, still, while Taku and Chiyu would normally serve as a support network, his personal issues end up causing him to distance himself from them, damaging the two longest-running friendships he's had.
Chiyu also has a rough time, particularly as she watches her two best friends changing and drifting apart from her. She dates Taku in the hopes that it will help things stay the same between them, but is jealous that Haru ended up being helped by Kuroyukihime, who seemingly doesn't treat him as an equal, while Chiyu herself could do nothing.
When Kuroyukihime's injured and on the brink of death, her parents don't even bother to show up, and simply send a lawyer in their stead, giving the first indication of how unhappy Kuroyukihime's family situation is.
Volume 2
Immediately after performing a Mercy Kill on Cherry Rook, Scarlet Rain tells the story about how they met at a boarding school, where Cherry became her first friend, as well as her parent and mentor on Brain Burst. She then admits that she realized, too late, how he wanted to always be her parent, and regrets not telling him that levels don't matter.
Volume 3
After Noumi defeats Haru and steals his flight ability, the source of Haru's confidence, both Haru and Chiyu are left broken- Haru over his defeat and inability to protect Chiyu, and Chiyu over how her hopes of restoring her friendships with Haru and Taku to the way they used to be had been dashed.
Taku confronts Haru over what happened with Noumi, but Haru, afraid of what will happen if Taku finds out, isn't able to tell him, leading to an argument between the two friends and Taku hitting him.
Volume 4
The revelation that Taku was severely bullied in the past, to the point at which he contemplated suicide. Apparently, thrusting attacks are such a severe Trauma Button for him that he has no hope of continuing kendo in high school.
Haru meeting with Chiyu, who, in order to keep up her facade of working for Noumi, is forced to act as though she betrayed him.
Volume 7
Saffron Blossom and Chrome Falcon's backstory. They wanted to create a world where players could enjoy the game together, since given that Saffron Blossom would likely die young, she could only live a full life in the Accelerated World. For their trouble, they end up being sacrificed to a powerful Enemy to be killed repeatedly, while many other Burst Linkers, their fellow outcasts in the real world, callously watch.
Volume 9
For a moment, Silver Crow thinks Black Lotus(actually Black Vise in disguise) betrayed him and is trying to kill him to remove the threat of Chrome Disaster. It doesn't last, but it's heartwrenching to see him trying to convince himself and the Disaster Armor that the person before him isn't Kuroyukihime.
Volume 11
Utai/Ardor Maiden's backstory. She wanted to be a Noh performer, but was not allowed to continue into adulthood, simply because she was a girl. Her older brother tried to intercede on her behalf, but was killed in a tragic accident with a mirror that traumatized Utai so badly that she lost the ability to use her voice for anything other than the Burst Link commands (which takes a great deal of effort on her part).
Volume 12
Kuroyukihime's backstory. Her older sister tricked her into killing Red Rider, thus destroying her own reputation and becoming a notorious criminal in Brain Burst. After confronting her sister with a knife, Kuroyukihime got kicked out of the house, while said sister got off scot-free. Shortly thereafter, Nega Nebulus raided the Imperial Palace and got forcibly separated. Because of a few bad decisions, Kuroyukihime lost almost everything.
Volume 13
Haru is forced to come to grips with the fact that the only way to save Rin from the side-effects of the parasitization of Ash's motorcycle may be to use the Judgment Blow on Ash Roller. That would be bad enough in most cases, but considering that Ash is his separate individual, it's essentially killing him.
Volume 21
Megumi's situation in this volume. She gets her Duel Avatar and memories of Brain Burst back, and is manipulated into thinking that if she helps the White Legion, her Parent, Saffron Blossom (who's almost certainly dead in real life) can come back. Haruyuki is forced to make her understand that her wish will never come true, and Megumi realizes that her betrayal might end up destroying her friendship with Kuroyukihime. Small wonder that Megumi nearly goes into Zero Fill when the truth hits her.
Volume 25
When Haruyuki starts to write a campaign speech, the first thing that comes to his mind is how much he hates himself and still blames himself for pushing Chiyu and Taku away. This shows that his self-esteem problems still plague him even after all the friends he's made and all the feats he's accomplished.
