I have my own opinion on this subject, essentially I don't believe that the aircraft was retired without a manned replacement, but I have also recently come across another twist on this theory - Aurora doesn't actually exist, it's a smokescreen for the real project and the SR-71 coming out of retirement is part of that smokescreen.
Back in 1963 the US unveiled the YS-12 Blackbird, which was redesignated as the SR-71 when it entered production. This aircraft was one of the most outstanding achievements in aviation history. Here was an aircraft that could fly so high and so fast that it could enter Russian airspace any time it liked, unchallenged. Even to this day it's maximum speed and range are still classified, though it is known that the SR-71 is capable of speeds well in excess of Mach 3.
Of course it wasn't that long before Russian missile technology caught up with the Blackbird, and indeed, they created the MiG-25 Foxbat-F, which was designed as an SR-71 interceptor, though none were ever intercepted.
The US countered this by redesigning the radar and cameras aboard the SR-71 so that they now took oblique angle pictures, instead of overhead ones. This alliance worked very well and the SR-71 is still in service today.
However, in 1993 the USAF took the unprecendented step of retiring the aircraft completely - saying that the satellites could do the job better and with less risk to personnel. But that's not whole story.
A satellite either orbits the earth on a fixed trajectory, or it is geostationary, that is, it stays over a fixed point on the earth's surface all the time. The problem with the satellites is that once they're in a fixed orbit it takes a long time, and a huge amount of energy to move them to a new orbit or location. If you need pictures in a hurry and don't have a satellite already covering the area you have a problem.
This was where the SR-71 was very useful. It is a very high speed aircraft (Mach 3+), and they are dispersed at airbases around the world, so they could get to any point on the globe in a short space of time. So how could the Air Force retire this aircraft without a replacement? I don't think they did.
For the last 7 years or so there has been much speculation about a project called Aurora. Of course the USAF and US Government deny the existence of this project, but they also denied the existence of the F-117A Stealth Fighter and B-2 Stealth Bomber for quite a long time. It is known that the F-117A was operational in 1988 as one of the aircraft crashed in Nevada, a crash which was hastily covered up by the military. This is quite a few years before it's admitted existance.
Aurora is rumoured to be a hypersonic (Mach 6+) aircraft, probably intended as an SR-71 replacement. To date, nobody has been able to get a photograph of the aircraft, though a number of people have reported strange sounds in the sky and a strange contrail appearing, which looks like doughnuts on a rope. It is thought that this unique contrail is produced by a new engine design, called pulse-detonation.
Of course the USAF has now unretired the SR-71. This may be due to technical problems with the Aurora or it could be to diffuse public speculation and interest in the Aurora project.
At a guess, I would say that the Aurora aircraft, if it does exist, is based in Area-51, the cordonned off section of the Nevada desert. This is an unusual place, as it has extremely high security, with warning notices threatening the use of deadly force against trespassers, but yet the US Government deny anything unusual happens there. To me, that just doesn't add up - we've seen them lie before, so why not do it again?
I was quite happy with my own theory on the SR-71 until very recently, when I was pointed in the direction of an article in the respected British military aviation magazine, Air Forces Monthly. The article related the story of an aircraft crash at Boscombe Down in Wiltshire, England. Boscombe Down is a UK Ministry of Defence (MOD) airfield to which the public, including civilian pilots, are not normally given access.
Normally there would be nothing too unusual about a aircraft crash, except the fact that it crashed which would almost certainly be reported in AFM anyway, but this one was very different. Within minutes of the crash the aircraft was covered with a large tarpaulin and then hauled into the privacy of a nearby DRA (Defence Research Agency) hangar.
Another aircraft was moved out of the hangar and the doors remained open long enough for an observer to catch a glimpse of the stricken aircraft as it lay in the hangar. It is reported that the aircraft was only half covered by the tarpaulin and that it's notable features were twin, inward canted, tail booms and a very flat nose section.
Unusually for Boscombe Down, a USAF C-5 Galaxy transport arrived within 24 hours of the crash. Most unusual was that the flight left the USA bound for Frankfurt-am-Main in Germany, but requested a diversion to Boscombe in-flight. The C-5 was backed up to the DRA hangar and it left for the USA shortly afterwards - never having gone to Frankfurt. Was this a cover-up on the flight plan, so as not to announce the destination as Boscombe Down?
AFM speculates that the crashed aircraft was not Aurora. Instead they believe that Aurora, while it may have existed at one point, is not a production aircraft. They suggest that the Aurora project was used as a technology demonstrator and test bed for the actual production aircraft, the Colt, which it also suggests, is a derivative of the failed Air Force tactical fighter, the Northrop F-23.
For the full details on this intriguing story, read the article at Air Forces Monthly's web site.