
As Doberman said, now that the pacifista have been disabled, the VAs now have their chance to kill Bonney.
At the moment, the SHs are in a massive peril, the 5 elders are gearing up to probably destroy the entire Labophase in order to prevent Vegapunk's message from getting out. This is obviously a problem, as the SHs are currently in the labo.
I think Bonney will be the solution to the problem. The VAs will attack Bonney to try to kill her. Having seen what Nika is actually like, Bonney will use her powers to actually become Nika. Whereas Luffy alone couldn't revive the ancient robot, the combination of Luffy and Bonney's heartbeats will start the robot, causing it to attack the gorosei, saving the SHs.