Battle Planet
- Shun, an 11-year-old, gets disowned by his father, after saving his friends from Masato, this all after his cousin attempted to murder him to take his place as the Kazami's heir and while his father was using his own son as nothing more than an information tool. Thankfully, he's able to leave with Wynton until the time being, but still.
- In Episode 65: A Devil on Your Shoulder, The Awesome Ones' successful mission completely transitions on Magnus, physically taxed and drained from the Pyravian battle and Core Cell meltdown at the Kazami’s island. Jealous and saddened he was unable to even stop the meltdown while Dan did, Magnus staggers, once again doubting his motivations as he reveals he can’t even Bakugan-battle normally without the gauntlet AAAnimus provided for him.
- Meanwhile, the aftermath of what happened to him and Emily after the end of season 1a is clear. The two siblings, not even adults as of yet, are forced to live in an abandoned hospital with little supplies and food to live on.
- Magnus's desire for power grants him the Titan evolution, but slowly loses his sanity to the point he's becomes a puppet for Tiko. Dan can only lie to Emily about her brother's condition and hope they can get him back to the light.
- After Masato’s plan to get the core cell backfired hard and almost blew up everyone on the island, he escaped, only to find himself trapped in the Maze with no way to escape for ten years. He gives up all hope, he resigns himself to his fate, and chooses to die, even freeing Serpenteeze. Thankfully, Serpenteeze manages to convince him otherwise.
- Shun having to fight Ichiro just after learning that his father's narrowly survived losing the Kazami Fortress to Tiko.
- Thryno's death, holding on just long enough to give Drago access to his true form and memories as Maximus and asking him and Dan to protect Earth and Vestroia in his final moments.
- Philomena having to watch her brother commit terrible actions while being controlled by Tiko after the two spent their entire lives drifting apart and fighting each others.
Armored Alliance
- Ajit in general. He was left in an orphanage and hated his time there. When he left, he was nearly attacked by a rabid dog until Storm saved him and raised him as his own, not helped by the way Storm treats him from time to time given the latter's status as his sole Parental Substitute. Upon their falling out, things only get worse as Storm attempts to murder who is essentially his child, in part thanks to Haavik's influence.
- Mc Q's path to villainy. He was nothing more than a humble CEO spending all of his money resources to sell brawling devices for those who couldn't compete in Bakugan brawls normally until the Kazami's devices and Philomena's accusation of them drove him out of business. Combined with the ban resulting from Philomena's misuse of them, Tiko-Benton equipping his brainwashed army of adults to fight with them, and Shun's group exposing the dangers of his device being used for nefarious purposes by those shady corporations, all his energy and money went down the drain, forcing him to essentially become a arms dealer just to survive.
Geogan Rising
- The group are still missing their Bakugan partners after being separating from them for six months. Even with Drago returning, the others are still in hibernation.
- Wynton and Jenny Hackett bond over improving the Mobile Gate but as Falcron warns him, she turns out to be a spy for Reed in the end, and breaks his heart.
