A fanfic idea that’s been sitting in my brain rent free ever since rewatching TFP and listening to Willow Tree March just gave me more ideas.
What if Raf didn’t survive after being hit with dark energon. Au concept where Raf didn’t survive but ended up sticking around as a ghost, he can interact with objects but can’t be seen or be heard.
(I’m thinking of calling it “Old Ghosts”)
His ghost probably has a purple glow to him because of the dark energon. He actively haunts the autobot base but not in a malicious way.
Now for some ideas
What if he can’t leave the base and watches the base get abandoned once the bots leave, Miko goes back to Japan and Jack goes to college. He’s just left there all alone, his ghost growing old with him. (Match how he would look if he were alive, I imagine he would switch between what he looked like when died and how he looks when he’s older.)
Raf just watches from the sidelines, the grief everyone going through after his death. He can’t do anything about it. Fowler has to inform Raf’s mother of his death.
June refuses to let Miko or Jack near the base anymore after Raf’s death. They still secretly go when they can but their visits are far less frequent
What if he’s just stuck there until some unknown amount of years later and like Miko and Jack come back to the old base with sole paranormal stuff because they never let go of the fact that weird stuff happened after Raf died. They bring a spirit box and everything.
Jack and Miko would be like in their early twenty’s, and would take place during RID2015 maybe(?) if I were to place it in some kind of timeline.
Thinking of possibly a new member to add to the duo. They’d be a spirit medium, and probably the catalyst  of everything after being able to hear and see Raf. I imagine it’s an annual thing to visit the base again for the pair.
Raf can’t leave the base at all since he died there and all his keepsakes were taken and he wasn’t able to attach his soul to them so he could go with them. If he tries to leave the base it’s like hitting an invisible force field. 
Miko and Jack would keep in touch with the bots once ratchet figured out how to create devices that were small enough for Miko and Jack to use. They keep in touch with most of the bots.
I’m so tempted to write this. I have so many ideas for it