All the girls......Elda (Chii) & Freya (Dark Chii) They are so pretty...also its sad that Freya shut herself off permantly

why did she do that?

because she was jealous of their mom

"because she was jealous of their mom" ... Wow, sounds like YOU read the manga properly. -_-; She shut herself down because she loved her creater so much and yet didn't want to come between him and his Someone Just For Him. She wasn't jealous AT ALL. She loved them both so much she essentially died of a broken heart.

and Fureiya's program was still in Chii so when Chii died, fureiya's program took over. then she asked Chitose to delete them both,Chii was still there her program was hidden she had realized that there were somethings only a human could for hideki)so she did. But hideki loved Chii and told the pasokon that if she knew where chii was to tell her the true meaning of happiness then the pasokon(Chii's body. now it was a pasokon because fureiya wasnt there nor Chii) started crying and Chii's program reloaded!

One of the most touching scenes in the whole series there, though I'd vote for Chii asking the BAkery guy about how saying godbye makes someone's heart hurt?