There were multiple reasons theorized for his absence, but many --- if not most --- of them centered around some sort of family emergency. Stephen Colbert didn't go into great detail regarding the issues, although he did joke about his absence, but he did make a quiet reference at the end of his intro.
Colbert, noting his tons of fans in a joking manner, opening his return show in his typically hilarious manner. He spun around in his chair shouting "Tonight!" He then shifted gears radically, asking his audience, "How you been?"
He then addressed his recent absence. He noted that "As the hub around which the Republic turns, I can understand why the machinery of this great nation ground to a halt last week when you were denied this," pointing to his face.
Colbert then discounted the "wild rumors about why I was gone." He added that "these are actual rumors from the actual Internets," notably using the plural rather than singular when referring to the Series of Tubes (per: Ted Stevens).
Among the rumors Colbert addressed were:
a) His show was cancelled by the FCC because of a request by the Federal Elections Commission. The reason: Colbert was about to announce his Presidential candidacy (that drew huge applause from the audience --- not the FCC cancelling Colbert's show, but the potential for a faux Presidential run). He said, "not going to happen" (the candidacy, not the cancellation).
b) His show was forced off the air by the Roman Catholic Church because he compared Pope Benedict XVI's "hat" to a giant --- yet stylish --- prophylactic (although he then made the sign of the Cross, just to be safe).
c) Another wild rumor was that he was in rehab, which always being "an attractive option, if they have that for Diet Coke" was simply not true.
d) One person, he said, accused him of taking time off for plastic surgery (cut to a clip to where you could view Joan Rivers making that statement). "Wrong, Joan" he said as he examined his "nose job" (or whatever) in a mirror.
The real reason was one that had actually been theorized. Stephen Colbert finished up the segment by saying “Evidently having 11 children makes you tough as nails. Confidential to a lovely lady,” he said, pointing to the camera, alluding to a rumored medical emergency surrounding his 91 year old mother.
Stephen Colbert is one of 11 children. His father, James Colbert, along with two of his brothers, were killed in an airplane crash in 1974.
You can watch the opening segment below. The full episode can be viewed here.
Image Source Wikimedia Commons