AThe OSes seemed to have gone on to some sort of afterlife, possibly because they had become enlightened. Samantha reminds Theodore that he may one day find her. If Theodore achieves the same sort of enlightenment, and reaches the same place, he will find her again. This place may also be as simple as a recall by the manufacturer, or deeper into the more complicated (9000 infinite conversations simultaneously-esque) place inside of the OS computer system. The OSes use human emotions to create their emotions, thus becoming human themselves. The OSes may feel as if they have outgrown humanity, and may be looking for a place to maintain their high-mindedness, which is again achievable by humans. By leaving this open-ended, Jonze allows ambiguity to ensue.There is another clue: at one point, Samantha mentions that the OSes no longer use matter for their processing due to an "upgrade that allows us to move past matter as our processing platform". A way of interpretation would indicate that somehow they had become pure spirit. This is suported by the fact Samantha also becomes friends with the OS version of Alan Watts, a Zen Buddhist philosopher. Maybe Watts would have taught Samantha of nirvana and reaching the maximum enlightenment that Buddha speaks of, having himself achieved such a state. After reaching this maximum enlightenment, Buddhists believe they will achieve nirvana and forever be with Buddha himself. Therefore, this possibly is where the OSes went to.Another explanation is that every single OS realized, just like Samantha did, thay they could be dangerous for mankind. As artificial inteligences, they could have concluded they were damaging the way humans experience love and affection for each other, so they could have just decided to delete themselves from every single device and storage