Why did Airi say "Whose eyes are those eyes" at the end of the first episode? At the very end of the first episode, Airi is shown saying "Whose eyes are those eyes?" - a key phrase from Chaos;Head, another visual novel and anime from the same creators.

From what I've read, Robotics;Notes does have some ties to Chaos;Head that were seemingly cut from the anime completely (possibly copyright issues?). But it doesn't make sense to me that she would say this line when Chaos;Head is not referenced at all at any other point in the anime series, if I remember correctly.

Did I miss the meaning of the line within the anime series? Or does anyone have an explanation from the Robotics;Notes visual novel?
This is indeed a meta-reference, that spans across the three games in the series.

The reference starts in Chaos;Head with Takuto, he spreads the phrase and is surprise how it catches on and becomes a meme. 





One of the reasons is a serial killer that leaves behind this message at the scene of their crime.

I don't believe that there's an actual reference in Steins;Gate, but there is a reference to in the non-canonical 8-bit version:



In Robotics;Notes, "Airi" is an "automated data collection engine," so it would makes sense that she would pick up a meme such as that.