Well, one possibility is that Dark Naruto would be overjoyed. After all, Kushina is his mother. But at the same time, he could be very conflicted. His dark side might make him suspicious of her motives. He could test her in various ways to see if she's really who she says she is. And Kushina, on her part, would probably be heartbroken to see what her son has become.
She might be overjoyed. After all, Naruto is her son. She could immediately rush to find him and embrace him tightly, tears of happiness streaming down her face.
Loki could be surprisingly empathetic. He would see a bit of himself in Peter, perhaps, as someone who has been misunderstood. So he'd try to befriend Peter and give him advice on how to handle the bullies without using violence, like using his intelligence.
It depends on how they left things before Clark was thought to be dead. If they were on good terms, they might quickly become close again. But if there were unresolved issues, those could resurface and make things difficult.
In the fanfiction, Loki could take Peter under his wing. He has a lot of power and knowledge, so he might train Peter to be more confident and able to defend himself. Loki might also use his magic to make Peter invisible when the bullies are around, so Peter can avoid them until he's ready to face them. And Loki would definitely give those bullies a stern warning in his own menacing way.
I'm not very familiar with this specific fanfic. However, generally, a fanfic about Loki and Thor might explore their complex relationship in the context of the Marvel universe. If Loki is intersex in this fanfic, it could add an interesting layer to the character's identity and how they interact with Thor.
If Thor finds out about Civil War fanfiction, he may also start to question the nature of reality and how Midgardians perceive the events that happened. He might wonder why they would create these alternate stories. He could even get interested in the creative process behind fanfiction and start to think about how his own stories could be told in different ways. This could lead to him interacting more with the creative community on Earth, or at least being more aware of their existence.
When Thor is mean to Loki in fanfiction, it can lead to a downward spiral in their relationship. Loki, feeling constantly attacked, may lash out in more extreme ways. Thor, on the other hand, may double down on his meanness, believing it's the only way to deal with Loki. This can create a cycle of animosity where any love or brotherly bond they had is overshadowed by anger and distrust. For example, Loki could start to form alliances with Thor's enemies out of spite, and Thor would see this as confirmation of Loki's untrustworthiness, making the relationship even worse.
There's 'Thor's Redemption in Loki's Arms'. In this story, Thor realizes his true feelings for Loki after a series of events that nearly tear Asgard apart. It's a tale full of emotion and character development.
Thor might initially go into denial. He can't believe that Loki is truly gone. He may hold Loki's body for a long time, as if waiting for him to come back to life. Then, he could become angry. Angry at the situation, at whoever or whatever caused Loki's death. Eventually, he may find solace in the memories of Loki. Remembering the good times they had together and using those memories to move forward.