Just like that, the CP9 agents from the original story were more or less wiped out.
The reason it was only "more or less" was because Kalifa had not joined CP9. Most CP9 agents had been trained from childhood, but there were exceptions everywhere, and personal connections existed everywhere too. The World Government had ruled the world for eight hundred years; it had rotted to the core, and its intelligence agencies were naturally no exception.
Kalifa was not an agent trained from childhood. She was a bona fide second-generation spy!
Her father had been an agent since his own generation, which was why she had been placed in CP9 in the original story. But now, her father was actually working for the Dragon Hunting Pirates. The World Government's intelligence agencies had nearly been hollowed out by Doflamingo. Even CP9 had only been spared because Doflamingo had deliberately left it for the Straw Hat Crew and wanted to cultivate some fresh meat of his own. Otherwise, he would have infiltrated them too.
Under such circumstances, Kalifa's father would never have placed his daughter in CP9, an organization full of cannon fodder.
—Incidentally, Robin had long since avenged herself. Spandam and his father had disappeared while carrying out a mission long ago.
In any case, those CP9 agents were all minor characters. Even if they might be promoted into CP0 in the future, they meant less than nothing to Doflamingo.
With the CP9 agents out of the picture, the Straw Hat Crew found themselves facing the combined forces of Gecko Moria and Sand Crocodile.
Just like Sand Crocodile, Gecko Moria was an enhanced version of himself now. In particular, Doflamingo had plenty of pirate corpses under his control, all of which had eventually been handed over to Moria to create a zombie