We learned via flashback that Rumple and Pan grew up "incredibly close," but now the lad's "darker and more repulsive" than anyone should be exposed to. No one can leave Neverland without Pan's permission. And in addition to leaving secret messages, Squid ink can also immobilize someone with just a single touch.
In the present day, Rumple and Neal reunited on the island and used the ink to freeze Pan and then took out the Lost Boys with a sleeping spell. Just as Neal and his sleeping son were about to meet up with Emma and the group, that super sneaky Pan caught up with him. In the final moments of the episode Henry finally woke up and said to Pan that he "dreamed" that he heard his dead father's voice.