WARNING: The following contains spoilers for Fantastic Four #26 by Dan Slott, R.B. Silva, Jesus Aburov and VC's Joe Caramagna, on sale now.
Franklin Richards has been having a rough time lately as his powers seem to be fading, and he has no idea how to get them back. Things just got worse for him when Professor X banned him from returning to Krakoa.
According to Xavier, Cerebro informed him that Frankin Richards is not, nor has he ever been, a mutant. This revelation adds a new dimension to the story of Franklin Richards, who has already begun to suffer signs of depression after the loss of his powers.
This might come back to haunt the mutants of Krakoa. When the mutants first moved to Krakoa, they set up their own government, created their own laws concerning mutants, and eventually faced off against the Fantastic Four. The First Family was battling Mystique and Sabretooth when Cyclops showed up. While it was a nice friendly meeting at first, things got tense when Cyclops said they were taking the mutants back to Krakoa with them. Then, despite the friendly undertones, Cyclops made an offhand comment that Franklin had a home in Krakoa when he was ready.
This didn't go over well with Franklin's parents. However, they made peace with it in Chip Zdarksky, Terry Dodson, and Rachel Dodson's X-Men/Fantastic Four #4, when Franklin officially decided to explore his mutant roots in Krakoa. However, with the new revelation by Professor X, that has changed. Franklin is not only no longer welcome, but Professor Xavier said the X-Men wouldn't be able to help him figure out what happened to his powers. With Xavier shutting out Franklin, he has turned away one of the team's most powerful allies, at least when Franklin is fully powered. This also isn't the first time that the X-Men's new isolationist ideals have led to the rejection of an ally.
In Deadpool #4 by Kelly Thompson and Kevin Libranda, Wade Wilson learned that he did not have access to Krakoa because, despite the misconceptions, he also is not a mutant. Deadpool couldn't get through to Krakoa and ended up sneaking in, which resulted in a giant fight. Emma Frost told Deadpool there is no cure for his cancer in Krakoa, and he is no longer welcome without a special invitation. She also pointed out that his unpredictable nature makes him a liability to Krakoa. In return, the current king of the monsters banned the mutants from Staten Island as well.
The X-Men took one of their most capable allies in Deadpool and alienated him, possibly turning him into an enemy in the process. They have now taken one of the most powerful heroes in the Marvel Universe, Franklin Richards, and banned him from their island. The X-Men have become a literal island unto themselves, and the dream of Professor Xavier to find a place where mutants and humans can live in peace has now become a nightmare of segregation and discrimination. As a result, The X-Men might have no allies to call on if they ever need help in the future.