A group of rogue shinobi from a small, unknown village might be behind it. They could be jealous of Konoha's power and saw Naruto as a way to gain an edge. They steal Naruto at birth, thinking they can use the power of the Nine - Tails to make their village strong.
It could be Orochimaru. He was always interested in powerful jutsu and having Naruto, who is the Jinchuriki of the Nine - Tails, under his control would be a great asset. He might have planned a secret mission to snatch Naruto at birth for his experiments.
The Akatsuki could also be responsible. Even though in the original story they started to target the Jinchuriki later, in fanfiction, they could have been more proactive. Maybe they had a prophecy about Naruto's power and decided to take him at birth to prevent him from becoming a threat to their plans.
It could be Death Eaters. They might have finally found a way to capture Harry without alerting Dumbledore. His 16th birthday could be the perfect opportunity as everyone might be a bit more relaxed thinking he's not quite of age yet for the full - on final battle.
It could be the elders of the Hidden Leaf Village. They might see Naruto as a threat to their traditional way of ruling. For example, if Naruto starts to question their decisions too much or tries to bring about radical changes too quickly, they could conspire to have him executed.
There's also the possibility that it was an accident. Some kind of jutsu gone wrong during the sealing process. The person performing the sealing might have been inexperienced or there could have been some unforeseen interference that led to Naruto being sealed away instead of the Nine - Tails being properly sealed within him.
Sasuke could be responsible. Their relationship has always been complex. Maybe in this fanfiction, their rivalry escalates to a point where Sasuke accidentally kills Naruto during a fight at the Valley of the End.
It could be a rogue ninja from another village who has a vendetta against Konoha. This ninja might have a special ability to target Naruto specifically and put him in a critical state.
One reason could be that he feels burdened by the expectations and the weight of his newfound peacekeeping role. He might want to escape the constant pressure and find himself. Another possibility is that he discovers a new threat during the post - war reconstruction and decides to go into hiding to investigate it without causing panic. Maybe he also has some personal issues related to his relationships, like feeling estranged from his friends who have changed after the war, and he needs time alone to sort things out.
It could be Orochimaru. He is always on the lookout for powerful specimens to experiment on or train in his ways. Naruto, as the son of the Fourth Hokage, would be an extremely appealing target for him at birth.
It could be a powerful dark wizard in the Fairy Tail world who mistakes Naruto for a threat. Maybe they sense his chakra and think it's some kind of dangerous magic they need to contain.
The village elders are likely candidates. They are often shown to be power - hungry and manipulative in the Naruto series. They might see Naruto's power as a threat to their control over Konoha and thus plot against him, which could lead to Naruto feeling betrayed.
It could be Orochimaru. He's always been interested in power and experimenting. Maybe he sees Naruto as a perfect guinea pig to test some new jutsu that goes horribly wrong and causes Naruto to explode.