A valid question, which is the heart at some of the anti-C. Cross arguments is the absolute lack of Magus/Janus (which is, quite honestly, a travesty). I've heard people make the assumption that he's dead, but I doubt that seeing as Lucca's letter addresses him.
I've always believed that he was stuck in 12,000 B.C., still looking for Schala. *How he was supposed to have gotten to 1020 to read that letter is beyond me.
*If I recall correctly, the Epoch was destroyed against Lavos' shell in the ending that Cross followed, meaning any sort of natural time travel was impossible since the Gates vanished. This also leads me to the theory that if Schala did go back to find Janus after being freed from the TD, she'd be stuck in that age, and thus unable to find Serge. (Thus the by saying "I" in the ending, she's referring to Kid, whom is technically "her").
That leads me to wonder though. When Schala was freed, where would she go? To the era she was freed in (which makes sense), to the era she was originally lost in (which also makes sense), or to wherever her little heart desired (which, I suppose, could also make sense).