Cloning. I mean if they can replicate food out of virtually nothing, and we can clone similar animals today, so why couldn't they clone them from old whale bones in an old museum? DNA has a 500+ year decay rate and ST was only set about 200 years or so from when whales went extinct. Sure, the Earth would have run out of power and there were terrible storms but from what I saw, cities weren't being swept away and large numbers of people weren't being killed. When the sun came out, everyone was a bit drenched but San Francisco looked nice and clean. Sure, they'd have had to cook their own food and shiver for awhile, but that's life. (Makes a pretty crappy movie, though.)

Also, they had samples of whale songs in the KLINGON database--I mean, that is the ship they were flying and they didn't exactly bring their iPads--so why wouldn Earth's "memory banks" have had the recorded whale songs from hundreds if not thousands of hours of research we've conducted in the 20th century? If the Universal Translator can translate languages from beings we haven't even met yet, why can't they run it on old whale songs until they could understand the alien's transmission?

This is the problem when you analyze sci-fi movies. Plot holes are often a mile wide. But we don't go to movies for the realism.

PS. How stupid would an alien species have to be to park a probe above a planet to check up on an old friend but when they received no reply, they just leave it in orbit to keep wreaking havoc? I mean, if you dial a phone number a few times and you don't get an answer, most people just hang up and stop calling.

Warp speed collision course straight into the alien vessel. No more whales threatening the planet.

Friggin' whales, man.

@manfromatlantis said:

How would they of brought the whales back,.

I don't get the question - are we saying that only the Klingon vessel could do the Superman flying around the sun trick?

They would just go back in time another way...probably with the Enterprise herself and land a shuttlecraft in San Francisco. A Klingon Bird of Prey wasn't the only way to go...although the fact it was lighter probably made it easier.

They probably could have temporarily used the bowling alley on board Enterprise to store the Whale tank.