This was very well done. One note if you choose to edit this for the archive:
In this line: "Lois set her jaw and said nothing. Her blazing eyes said it all. Clark sighed and stood. He padded to the window that he always entered in when he was in his super disguise. He stood for a long moment, leaning on the sill and gazing out at the city that he proudly called his home. The city he would leave if Lois chose to reject him," you switch briefly from Lois's POV to Clark's. You might want to make that clear very early in the line or keep it from Lois's POV. I did a double-take because I assumed it was still Lois's POV and I thought she must know his secret already.
Very clever story. I enjoyed it a lot.
Happy
