That eukaryotes were designed from preexisting microbes by an alien intelligence (perhaps as part of a terraforming project or something along those lines) would explain that better than evolution. Not that evolution couldn't have done that, just that ID fits the evidence as well or better.
Let's follow this through logically and scientifically.
Evidence - The development of eukaryotes was very sudden. (note: By
sudden we still mean several 10s of millions of years at least but this can be termed sudden by evolutionary standards)
This can be explained by 2 (at least) possible mechanisms.
Hypothesis 1 - Inteligent aliens caused the modifications.
Supporting evidence - None. No direct evidence of this has been found.
Circumstantial evidence - None. We don't know whether any other alien race exists or has ever existed. No evidence of them has ever been found.
Hypothesis 2 - Evolution got a bit lucky and made a breakthrough by pure chance.
Supporting evidence - None. No direct evidence of this has been found in the fossil record.
Circumstantial evidence - Evolution happens. We see it happen all around us every day.
From these two possible scenarios we see that evolution is by far the most probable explanation because we know that it happens to this day. Although we cannot directly test what happened during the cambrian, by extrapolation it is possible to see that it could well have happened this way.
Furthermore, assuming that the aliens were not God (no beginning or end etc. yada yada), then they themselves must have evolved somewhere else. Further evidence that evolution
can go from nothing to a sentient being.
In the absence of absolute proof either way,
the principle of parsimony (or Occam's razor) states that we should always choose the answer with the least complexity.
In this case, the addition of any kind of inteligence is increasing complexity. It is completely unecessary and must therefore be rejected, pending further evidence.