Card Captor Sakura – You Were There (Ico Ending Theme) lyrics

The lyrics are probably written out of Yorda's perspective, "you" referring to Ico.
"Nonomori" apparently translates to "Thank you" in Yorda's native tongue (a fictive one without real translations, so this can just be guessed) . She uses this expression towards Ico in the video game as well.

//The following part contains spoilers//

//If you are not familiar with the story of Ico I suggest you inform yourself as I am not gonna explain the story itself (except the ending)//

The song plays in the end of the game.
After you defeat Yorda's mother (who said Yorda would never escape the castle) and she no longer possesses her body the castle collapses and Yorda is transformed to a kind of shadow. This black silhouette rescues the consciousness Ico (who was knocked against a wall before), herself remaining in the castle. Ico awakens on a beach, finding Yorda there (alive).

The lyrics seem to imply, that Yorda lost her memories after this incident ("Fleeting memories rise from the shadows of my mind [...] Though forgotten all promises we keep"). Still her subconscious tells her she knows Ico, who was helping her, although he had no reason to, even risking his life. Seemingly she fell in love with him ("How to define the way I'm feeling / You were there"). She remembers herself being grateful (repeated use of "nonomori")‎.

Now everything else I will leave up to you. Some parts of the text are either obvious or too vague for me to interpret. I you got a theory post it!