Your eyes
As we said our goodbyes
Can't get them out of my mind
And I find I can't hide
From your eyes
The ones that took me by surprise
The night you came into my life
Where there's moonlight

I see your eyes

She always wound up thinking about that night, when he tried to get her drunk and fire her, have sex with her. She knew she had made the right decision, going home alone, but she couldn't help wondering what might have happened if she had let him come with her. So many things reminded her of that night, it seemed as though she never stopped thinking about it.

How'd I let you slip away
When I'm longing so to hold you
Now I'd die for one more day
'Cause there's something I should have told you
Yes there's something I should have told you

She should have accepted him, that day at the airport. She now recognized the feeling in her stomach as love; wished time travel were possible so she could let Daisy go on a fruitless search in the Maluku Islands without her, so she could beg Booth to stay state-side. He didn't need to go to Afghanistan, risk his life.

When I looked into your eyes
Why does distance make us wise?
You were the song all along
And before this song dies

Even though she knew rationally that looking into a person's eyes doesn't tell you if they love you or are lying or any of that nonsense, she felt she could tell that Booth really cared about her more than he should. She waited for him on the National Mall by the coffee cart, hoping he had been able to make it.

I should tell you I should tell you
I have always loved you
You can see it in my eyes.