Let us analyze the facts:

1) The breakup occurred at a very great height, over 40 miles.
This excludes any possibility for the supposed Earth-based
attacker to shoot it down with existing land-to-air missiles,
as none of them are able to reach the height of even close to
40 miles. Others may entertain the possibility of an attack,
with the use of special missiles or laser guns, launched by a
Russian satellite, another space device, or a Russian high-altitude
strategic bomber (e.g. TU-95 or TU-160) that somehow could
approach or cross the US border.
Those who believe that this is the truth may use, as a kind of
"supportive information", the following fact: just about 20 minutes
after the crash, RosAviaCosmos, the Russian space agency,
declared that it  might have been caused by a technical defect.
But the problem is that some other specialists made their own
(different) claims in the same time period.

2) Some sources, including RosAviaCosmos, claim that a little
fragment of Shuttle's protective surface layer that had fallen off
the Shuttle during its start on January 16, 2003, caused the
formation of further splits, which then resulted in an explosion.
Other sources, however, claim that during the time the Columbia
was in the orbit, NASA specialists analyzed this problem and
came to conclusion that it couldn't influence the flight. This sounds
a bit odd, since unprotected areas can very easily get caught in fire --
because of air friction.

So actually, there may be two explanations for Columbia's crash:

I) Hot air friction sparked a fire in the damaged (unprotected) area
while Columbia was descending at a speed of about 3.8 miles per
second. The fire burnt through the unprotected area, and then
reached the internal areas of the shuttle, its engines and fuel tanks.

The problem with this scenario is that it could as easily have
occurred during the shuttle's takeoff, when its speed and air
friction were approximately the same as when landing, and
when the shuttle had much more fuel than during landing.

II) It was shot down by extraterrestrials. Maybe they didn't
use any weapons to crash it, but simply approached it in their
craft, causing Columbia's electronics and engines to fail
because of the effects of the alien starcraft's electromagnetic
fields. It also may be that an alien craft had approached the
Columbia without any malicious intent, but that its
electromagnetic field's effects on Columbia's electronics
and engines were unforeseen by the aliens.

This, however, doesn’t explain why the shuttle exploded in the
air, instead of merely plummeting to the Earth. Thus, the more
likely scenario is that Columbia was shot down by the alien craft.

On this photo you can see the trajectory of the Shuttle Columbia's fall.

If so, the question arises: what did the aliens wish to show mankind
by their action? Possibly that oil-based engines (which are used even
by such advanced craft as space shuttles) have almost reached their
peak effectiveness and reliability -- and that it is time to develop and
actively use alternative and more reliable engines. Today's weapons
and missiles, which are much less effective than ray and/or laser
weapons, face approximately the same condition. (Some weapons
were reportedly tested by the Columbia's crew during the flight,
perhaps by the crew members who were simultaneously active
[non-retired] military aircraft pilots: US Air Force colonel Rick
Husband and Israeli Air Force colonel Ilan Ramon).

...But who can know for sure how all this occurred in reality?

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