One idea could be Loki, in his Jotun form, is initially feared by Thor but then Thor realizes that beneath the different appearance, Loki is still the same person he cares about. They could go on a quest together where Thor has to protect Loki from Asgardians who don't trust the Jotun form.
A possible plot could be that there is a prophecy about a Jotun - Asgardian union being the key to saving the Nine Realms. Loki, being Jotun, and Thor, as an Asgardian, are reluctantly pushed together by Odin. At first, they resist but as they explore the prophecy further, they find that they have a unique connection that might just be what the Nine Realms need.
A great aspect of Jotun Loki x Thor fanfiction is how their bond could develop over time. It might start as a simple friendship based on their shared experiences in Asgard. But as Loki discovers more about his Jotun heritage, Thor could be the one person he turns to for acceptance. Their relationship could then slowly transform into something more romantic as they realize they have a deeper connection than they initially thought.
Well, in Jotun Loki x Thor fanfiction, the power dynamics could also play an interesting role. Thor, being the mighty God of Thunder, and Loki, with his Jotun powers and cunning. Their relationship could be a balance of power, both physically and emotionally. Loki might use his Jotun abilities to protect Thor in some situations, and Thor could be the one to offer emotional support to Loki, who often feels alone because of his dual nature.
One plot idea could be Thor becoming overly possessive of Loki after Loki gets too much attention from other Asgardians. Thor starts to isolate Loki, thinking it's for his own good. Another could be in a situation where Loki is injured, and Thor's yandere side emerges as he refuses to let anyone but himself tend to Loki. A third idea is that Thor, in his yandere state, tries to make Loki dependent on him by controlling all aspects of Loki's life in the name of protecting him.
One plot idea could be Thor and Loki as younglings getting into mischief in Asgard's forbidden areas. Maybe they accidentally unleash a minor magical creature that causes chaos in the palace. Another could be a story where they compete in a friendly, yet intense, training tournament to prove who is the better warrior at a young age. And they could also go on a secret adventure outside of Asgard, defying Odin's rules, to explore a rumored enchanted forest.
By showing mutual respect. For example, Thor could respect Loki's Jotun heritage and not treat him differently. This would make Loki feel more accepted and in turn, he could open up to Thor more.
One idea could be that Loki and Deadpool are forced to team up by some cosmic entity. Loki is initially annoyed by Deadpool's constant chatter and antics, but gradually comes to respect his unorthodox fighting style. Another plot could involve Deadpool getting transported to Asgard and causing chaos, with Loki having to either clean up his mess or use it to his advantage. Maybe they could also be on a quest to retrieve a powerful artifact that has been stolen and is being misused in the multiverse.
One possible plot could be that Laufey, Loki's biological father, decides to use Loki against Thor. He might abuse Loki in some way, either physically or emotionally, to make Loki do his bidding, which could involve causing trouble for Thor. Loki, being in a difficult position, has to deal with his complex feelings for Thor while also trying to escape Laufey's control.
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.
Often, there's a theme of family and legacy. The baby could be seen as a new hope or a potential change for the future of Asgard or their family. And the whole situation might force Thor and Loki to re - evaluate their places in their family and the world. It's also common to see themes of sacrifice and love, as they face difficulties together due to Loki's pregnancy and they have to make choices to protect each other and the unborn child.
One common theme could be redemption. After experiencing abuse, Loki might be on a journey to redeem himself or find a way to heal. Another theme could be power dynamics. The abuse might be related to power imbalances between Loki and Thor, which can be explored in different ways. And also, the theme of forgiveness could play a role, either Loki seeking forgiveness from Thor or vice versa.