Had a thought for a potential "Bad End" had Jun not rescued Motoko from Maelstrom in time during the war arc:
Note: words in italic are text messages
*Several months after the Tiger Claw/Maelstrom war*
"Heads up V," Regina Jones started. "I've got another Cyberpsycho sighting near your location. Be careful, this might very well be a double feature. Sending you the deets now."
No sooner had she hung up than did V's text notification start ringing.
Subject: Jun Kusanagi and Motoko Kusanagi
Last Sighted: 12 hours ago near the Northside Docks.
Several months ago, a major gang war broke out between the Tiger Claws and Maelstrom. Maelstrom had an initial advantage with their chrome, so the Tigers formed a special combat group called the Kamikaze, consisting of front line fighters chromed up to the very limits of what they could take and kept in line with strict discipline. Jun was a prolific member of this group, with his ferocity in battle earning him the moniker "Oni".
Maelstrom decided that they needed to make an example of the Oni, so they kidnapped his younger sister, Motoko, and planned to set up an ambush for him. However, the bastards couldn't just leave her be while they waited, so they made a sick game of it, making the girl take part in blood sports and then forcibly chroming her up between fights.
Jun and the rest of the Kamikaze did eventually rescue her, but by that point the damage was already done. Her body was more chrome than flesh, and her nervous system was nearly fried from the botched job the maelstrom ripper did.
After the war settled down and a peace accord was drawn up, both of them completely dropped off the radar and nobody's seen or heard from them since, until yesterday, when Jun was spotted abducting a local ripperdoc.
V sighed as she pulled out her tranq pistol. She had a feeling in her gut that this gig was gonna be an absolute bitch.
*One Epic, City Block Destroying Battle and Investigation Later*
V: Hey Reggie, I managed to find and subdue the Kusanagi siblings. The brother was apparently trying to get help for his sister, but when the doc gave him her prognosis, he snapped and ended up slamming her through a wall. Sending you the video file now.
*A little while after that*
Regina Jones: Hey V. Just thought I'd give you an update on the Kusanagi siblings. My people managed to pick them up before Maxtac showed up. It took some time and a team of surgeons, but they managed to remove all of the Maelstrom chrome from Motoko and replace it with less intrusive and properly connected implants to help mitigate the damage. While it's doubtful she'll ever make a full recovery, she's proven herself to be quite resilient the doctors are hopeful that she'll at least eventually be able to live a normal life.
Jun's a different story however. He's completely shut down and gone fully catatonic. The docs are saying it's purely mental, most likely trauma from believing that he failed to save or protect his sister. They're hoping his condition will improve alongside Motoko's, but at this point, only time will tell.
V: Glad to hear they're recovering Let me know if I can do anything.
Basically, the idea is that they went from heroes of their own story, to just another cyberpsycho side job for V to knock out in the canon videogame timeline.