SEASON 1

Their relationship is clear since the begin of the series.
Shirley fell in love with Lelouch due to an accident that happened after a bit they know each other. She's always unsure and hurried with him, but she always tries to do her best in order to have the big chance she always waits.
The first time they had a date was for a concert. Shirley's father gave her as a present two tickets, and, after talking with Milly (Sound Episode Vol. 1 track 3), she decided to ask him if he agreed to go out with her. She did it all of a sudden and never stopped to talk for a second, so, she told him all and went away (it was a YES XD). Unfortunately, the day of the date, in a battle, one of Zero's orders killed Shirley's father, and she was too shocked, but she waited for him to the place where they had the date. When he was there, she continued to cry and, hugging him, told him to save her, with a long kiss.

Lelouch loved Shirley very much and the fact that it was him the one who killed is father was oppressive. He tried his best to forget about this story, but it couldn't be helped. As if it wasn't enough, Mao, tried to tell her the truth, reading her mind and manipulate it in order to let Shirley kill Lelouch. There was a fight between the two of them. She shooted him, but at the end, her love was too big to kill him, even if he was his father's killer. It couldn't be helped, Lelouch decided to delete her memories about him and from that moment on, they were strangers.

Even if Shirley lost her memories, she found out a piece of her diary, where she wrote all the truth about Lelouch and his identity. She was astonished, and wanted to talk with him, even if 'till the end of the first season, she won't do it. At the end of it, she will believe in him, knowing that he won't ever betray his friends.

SEASON 2

(WARNING!! IT MAY COTAINS SPOILER!! PAY ATTENTION BEFORE READING!)

After one year, Shirley fell again in love with Lelouch. Even if she forgot ALL (because Charles di Britannia wrote new memories in her mind with his GEASS), she always trust Lelouch in all things he does.
In the third episode of this second season, she told him to buy a present for Viletta's birthday, and he asked to go out with her. A date? Yes, it was a chance! Shirley was very happy to go out with him, and, even if at the end it wasn't something REALLY special, the two of them seemed to be very close. She's always there, watching him and worrying about his life.
Anyway, their relationship change all of a sudden because of a question that Lelouch made to her. Shirley is the kind of girl that he prefers, and maybe, this reply, "the power of love" that she felt, was the thing that relates him the most to her. After that Lelouch went into the Chinese Federation and Sayoko took his place, there is a second kiss between them (Sayoko's kiss... -_- But he was Lelouch for Shirley's eyes).
For Milly's graduation, she made the "Cupid's Day", a game where boys and girls wore a heart-shaped hat that one of the two has to take and exchange with the boy/girl that they wanted to stay with. The couple who will exchange them would be official. At the end of the game, Shirley and Lelouch menage to do it, and before of changing them, Shirley asks why he kissed her. Since he doesn't know what to reply, Shirley told him that she would let him fell in love with her some day.

BIG SPOILERS FROM HERE ON

Yes, for the Ashford's students, they were a couple, but at the end of the 12th episode, happened something we've never expected to see. Jeremiah was back and his Geass Canceller deleted Lelouch's effect of Geass in Shirley's mind, letting her remember all about Lelouch's identity.

Even if she was shattered from those memories, Lelouch saved her life with Suzaku's help, and she understood that what she felt for Lelouch was true love. She wanted to stay with him and help him even if he was Zero, because she knew he was fighting all alone, and she wanted just his happyness.
Fate is always mean. When she was going to reach him, she met Rolo and after talking with him, she shooted her.

She will die in Lelouch's arms, revealing her true feelings for him and hoping that, when she will reborn, she will stay with him because their love was a never-ending one.
I personally think that Lelouch's love for Shirley was obvious at the end, and I hope he will remember her in the coming episodes.

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