One possible plot twist could be that the baby has some unique power that neither Naruto nor Tsunade possess. Maybe it has the ability to control time, which causes all sorts of chaos and also attracts the wrong kind of attention from villains who want to use the baby's power for their own evil deeds.
A plot twist could be that the baby is actually a reincarnation of an ancient and powerful shinobi. This would mean that Naruto and Tsunade have to protect the baby not only from the regular threats in their world but also from those who believe the baby's reincarnation is a sign of a coming apocalypse or a great change that they want to prevent.
In the fanfiction, Tsunade might rescue baby Naruto from a dangerous experiment that was being carried out on him. As she rescues him, she realizes that Naruto has an extraordinary ability to resist the negative effects of the experiment. This leads her to believe that Naruto is destined for something great and she devotes herself to protecting him at all costs.
A plot twist could be that Naruto discovers a secret about Tsunade that she has been hiding all along. It could be something related to her family or a power she has been suppressing. This discovery could either strengthen their relationship or create a rift between them. Also, there could be a twist where an outside force tries to use their relationship to gain power in the ninja world. They might try to manipulate Naruto or Tsunade to their advantage.
One possible plot twist could be that the baby has some unique magical abilities that neither Severus nor Hermione expected. Maybe the baby can communicate with magical creatures in a way no one has seen before. This could lead to all kinds of adventures as they try to understand and control this new ability.
One possible plot twist could be that the baby has some special powers or abilities. Maybe it's a super smart baby who can communicate on an advanced level from a very young age. This could lead to all sorts of interesting situations, like the BAU team using the baby's insights to solve cases in unexpected ways.
One possible plot twist could be that the baby has some sort of super - power that neither Loki nor Valkyrie expected. Maybe it can control time like Loki but also has the strength of a Valkyrie. This could put the baby in danger as various forces in the universe would want to either use or destroy it.
One possible plot twist could be that Itachi's past actions as a double agent in Akatsuki are revealed in a new light because of the baby. Maybe his enemies try to target the baby to get revenge on him, but Sakura, being a strong kunoichi, defends the baby with all her might. This could lead to a series of battles and alliances being formed in the shinobi world to protect the new life.
Perhaps a plot twist could be that Naruto's schizophrenia makes him see a different version of the ninja world. In his hallucinations, the villages are at peace and there is no war or conflict. This contrast between his hallucinations and the real, war - torn ninja world could make him question the purpose of the ongoing battles. He might then strive to make the real world more like his hallucinated peaceful world, which would be a really interesting character arc in the fanfiction.
One possible plot could be that Tsunade discovers baby Naruto alone and decides to take him under her wing. She could train him from a very young age, teaching him not only ninja skills but also important life lessons. Maybe she'd protect him from those who still hold grudges against the Nine - Tails within him. This would lead to a Naruto with a different kind of upbringing and a very strong bond with Tsunade.
One possible plot twist could be that Tsunade trains Naruto not just in physical combat like she did with others, but also in medical ninjutsu. This would be unexpected as Naruto is more known for his brute force. Maybe Naruto uses his new medical skills in a creative way during a battle, like healing his opponents to show mercy and then defeating them when they are off - guard.
One possible plot twist could be that Naruto's Mokuton abilities attract the attention of Orochimaru. He might try to capture Naruto to study his unique power. Since Tsunade raised Naruto, she would be extremely protective and engage in a fierce battle with Orochimaru to keep Naruto safe. This would not only test Tsunade's strength but also Naruto's growth under her care.