The Phantom Troupe could form an uneasy alliance with some of the more morally grey members of the Justice League, like Catwoman or Lobo. They might team up to take down a common enemy that the League can't deal with using their usual methods because of legal or moral constraints.
For Gon, his relationship with Chrollo would be crucial. Chrollo is the leader of the Phantom Troupe, and Gon's sense of justice might clash with Chrollo's leadership. However, Gon might also see some good in Chrollo and try to influence him in a positive way. Killua would likely form alliances with the more practical members of the troupe, like Pakunoda. She's smart and has a good understanding of the group's dynamics. Killua could learn a lot from her about how to survive within the troupe. As time passes, both Gon and Killua would have to adapt to the different personalities and values of the Phantom Troupe members, which would be a continuous process of give - and - take.
One possible fanfiction could involve the Phantom Troupe's unique abilities clashing with the superpowers of the Justice League members. For example, Chrollo's nen ability to steal other's abilities might be a huge threat to the League. Maybe he targets Superman and tries to steal his super strength. This could lead to an epic battle where the League has to figure out how to counter the Troupe's devious tactics.
One possible plot could be that Killua joins the Phantom Troupe in order to protect Gon. He might think that by infiltrating the troupe, he can keep Gon safe from their potential threats. Maybe he initially pretends to be on their side, but as time goes on, he starts to question his own actions and the morality of the troupe.
One interesting fanfiction could be 'Gon's New Path'. In this, Gon is raised by the Phantom Troupe but still retains his own sense of justice. It shows how his values clash with the troupe's more amoral ways. Another one is 'Gon Among Thieves' which delves into how Gon adapts to the troupe's lifestyle while trying to bring some positive change from within.
One common theme is identity. Gon has to figure out who he is while being raised by a group that has a very different moral code. Another theme is loyalty. He has to decide where his loyalties lie, with the Phantom Troupe or with his own sense of right and wrong.
They might bring a new perspective to the Phantom Troupe. Gon's unwavering sense of justice could influence some members to question their own actions. Killua's knowledge of the underworld outside of the troupe's usual scope could also be valuable. Maybe they would start to take on different types of jobs, not just the typical heists and assassinations. For instance, they could get involved in helping people who are being oppressed by other criminal organizations, which would be a radical change for the Phantom Troupe. But this new direction could also divide the troupe into those who support Gon and Killua's ideas and those who oppose them.
In terms of his relationship with Kurapika, it would be very tense. Kurapika is on a vendetta against the Phantom Troupe, and Killua joining them would put him in direct opposition to Kurapika. Killua would have to deal with Kurapika's hatred towards the troupe while also trying to keep his true intentions hidden. And with the troupe members, his relationships would be a mix of fear, respect, and secrecy as he tries to navigate the dangerous world of the Phantom Troupe while still holding onto his own values.