One possibility is that there could be a huge ideological rift between them. Maybe Steve discovers some dark secret of Tony's that he believes endangers the world in a way that can't be resolved through normal means, leading to the extreme act of killing him.
Some fans would be extremely shocked and disappointed. Steve and Tony are two beloved characters, and their relationship is complex and interesting. Killing one of them off in such a way would be a huge departure from what many expect.
One reason could be to explore the extreme consequences of their ideological differences. In the official story, they had disputes over things like the Sokovia Accords. In fanfiction, this could be pushed to the limit, leading to Tony taking Steve's life.
One possible plot could be a misunderstanding that leads Steve to believe Tony has done something extremely harmful to the team or innocents. For example, if there was false evidence suggesting Tony was secretly working with an enemy. Another plot might involve a moral disagreement that gets out of hand. Maybe they have different views on how to handle a new threat and Steve, in a moment of extreme passion, makes a terrible mistake.
In a 'Tony kills Thanos' fanfiction, the plot could start with Tony being haunted by his previous failures against Thanos. He decides to go on a solo mission to study Thanos more closely. He discovers a way to disrupt Thanos' connection to the Infinity Stones. With this knowledge, he devises a plan. He lures Thanos into a trap where he has set up a device that can nullify the power of the Stones. Then, in a tense battle, Tony uses his own advanced technology and combat skills to fight Thanos without the Stones' advantage and finally manages to kill him. This could be a story of redemption for Tony, showing his determination and ingenuity in the face of seemingly insurmountable odds.
Well, it's not super common but it does exist. There are different reasons for this kind of plot. Maybe the writer wants to explore the consequences of a breakdown in their relationship. They had their differences in the movies, like in 'Civil War', and some fanfic writers take it to an extreme by having Tony kill Steve to show how far things can go wrong when they can't resolve their issues.
Well, perhaps it could involve Tony dealing with the physical and emotional challenges of being pregnant in the harsh environment of Siberia. Maybe he has to find ways to get proper medical care while being in such a remote place.
Perhaps there's a power struggle over a new technology or a powerful artifact. Tony wants to use it for what he believes is the greater good, but Steve opposes him. Their clash escalates to a point where Tony, in a fit of rage or desperation, kills Steve. Or maybe it's a situation where Steve discovers some dark secret about Tony's business dealings and Tony kills him to keep it quiet.
Perhaps Steve leaves because of a personal sacrifice. He might discover that his presence is putting Tony and Peter in danger, like there's a villain targeting those close to him. So, to keep them safe, he leaves without much explanation. It could also be that he has some unfinished business from his past that he has to attend to alone, which forces him to part ways with Tony and Peter.
Perhaps in this fanfiction, Tony is kidnapped from Siberia by a powerful villain who has a long - standing grudge against him. The kidnapper could be after Tony's Iron Man suit technology. They snatch him from Siberia as it was a place where he thought he could be safe or was conducting some top - secret research related to his suit's power source. His friends then have to embark on a dangerous rescue mission.
One possible scenario could be that Tony is in Siberia on a mission gone wrong. Maybe he's facing a powerful enemy there, and despite his best efforts, he gets fatally injured in a fight. Another could be that the harsh Siberian environment plays a role, like he gets caught in a blizzard and succumbs to the extreme cold.