Another possibility is that a rival pirate group that has a long - standing feud with the Whitebeard Pirates managed to finally get the upper hand and capture Marco. They could have been studying his movements for a long time and found a weakness in his defenses. This group might be led by a very cunning and powerful pirate captain who has a personal vendetta against the Whitebeard Pirates and sees capturing Marco as a major victory.
Well, he might be used as a bargaining chip against the Whitebeard Pirates. His captors could try to extract information about the pirates' secrets or hidden treasures.
As I said before, it could be the Shredder. He has always been after the turtles and wants to get rid of them once and for all.
It could be the Blackbeard Pirates. Since they have a history with the Whitebeard Pirates, they might capture Marco to get information or as a form of revenge.
Maybe some of the more conservative village elders. They have always been a bit wary of Naruto because of the Nine - Tails inside him. So they might be behind his capture in the fanfiction.
Perhaps Marco uses his intelligence to outwit his captors. He could pretend to be weak or injured and when they least expect it, he could make his move. He has a lot of experience from his time with Whitebeard, so he could use that knowledge to find a weakness in their security and escape.
Maybe a rogue ninja group that wants to sell Naruto to the highest bidder. They see him as a valuable asset due to his strength and status in Konoha.
Maybe it's an old foe who has come back with a vengeance. For example, a gem that Steven thought he had defeated before might return and capture him in order to get revenge. This foe could have some new abilities or powers that make it difficult for Steven to escape.
It could be a rival group. They might be jealous of Serena's abilities or resources and capture her to gain an advantage.
One possible scenario in this fanfiction could be that Ace and Marco are facing a powerful and unknown enemy in a spooky, haunted island. The island is filled with strange noises and dark shadows. Ace's fire powers seem to be ineffective against this new threat as it keeps disappearing and reappearing. Marco, with his phoenix abilities, tries to scout from the air but gets caught in some sort of dark mist. They have to rely on each other and their friendship to overcome their fear and find a way to defeat this mysterious foe.
There's also a chance that an old enemy of the Thundermans, who has been lying low, resurfaces and decides to take revenge on the family by hurting Max. This enemy might have some new powers or a new plan that catches Max off - guard and leads to his injury.