Essentially the episode was all about dealing with Ai's trauma by having an alternate her as the Wonder Egg. Through this Alternate Ai, we see what COULD have happened to Ai had she not had friends available to her to fall back on. Feeling left alone to deal with bullying and even worse after her mom got together with the teacher she was suspicious of she takes the drastic step of drowning her self.

It's through this alternate Ai that we can see how far our Ai has come and it ultimate helps in being able to take down the Wonder Killer, that being a warped image of Sawaki-sensei made by the Alternate Ai. Our Ai knows his true personality due in part to how much she has grown.

In regards to Koito, it becomes clear to Ai that Koito was there at the right place and time for her, but she never truly understood anything else about her. This is what leads Neiru to label her as a "fake friend." She was important to Ai, but not the most important person to her now. But she was there when she really needed it, and we see the effect of what happens when she isn't.

This episode is probably one of my favourites just because of all these underlying messages that I'm sure I couldn't cover completely, but the analysis I linked does a better job than I ever could!