The other day I was watching an interesting film having to do with a strange structure erected in the wilderness under mysterious circumstances, and it reminded me of the first scene in .Hack//SIGN episode one - where we are shown a desert/beach or shore and the focus is given to a towering telephone or cellphone device that is shown erected in the middle of this unusual setting. The telephone has a screen and it turns Green. It is once again shown in the last episode of the series. This time the screen turns a bright red.
For a long time I did not understand the significance of that structure, and what the sudden colors meant. And then today I came up with a very possible explanation. (please consider that this is only a theory)
Throughout the series we see Tsukasa and Macha communicate with a voice, who is later revealed to be the program Morganna. And then, once the events transpired in SIGN come to an end we are introduced to the larger part of the story - the plot which follows in the IMOQ saga. However, during these events we can no longer hear Morganna. It can be argued that the reason for this is that there are no characters who have direct contact with the program like Tsukasa and Macha did during SIGN. I am not completely certain if that is actually true or not.
However, the point that I want to make here is that I believe the scene in which the phone screen turns green was merely a representation of Morganna's reaching out to Tsukasa. In much the same way that a cell phone may turn green to indicate that the incoming phone call has been answered, the green screen reflects Morganna's calling of Tsukasa in order to initiate her plans. And then, in the last episode of the series, when the phone screen is shown turning red, it may indicate that the "phone call" has ended - therefore there is no longer any communication between Morganna and Tsukasa. And perhaps, it may even represent Morganna's inability or decision to no longer directly communicate with anyone else. And that is why her voice is never heard throughout the IMOQ saga of .Hack.
Of course, this is just a theory. I don't claim to be right. But in my head this explanation makes a good amount of sense.