One interesting idea I've toyed with a few times is the arival of a teraforming "package" from space containing semi-biological, semi-nanotechnological organisms, that try and change the planet into a form more suiting they're alien originators.

Humans battle the growing alien forest-machine continously, but eventually realise that any method that would destroy the invader would also completely wreck the planet for them as well. But time is running out, and they have no other method they can implent quick enough. So they retreat as many people underground as they can, and Nuke 'em from orbit (it's the only way to be sure!). They then wait out the ensuing nuclear winter, and return to a much changed surface with the intent of rebuilding all they've lost.

Then the alien colonists arrive. Now, they were expecting to find a nicely teraformed planet, ripe for settling; but instead they find a mix of half transformed areas, mutated wasteland, and very, very, very pissed off humans. The aliens technology is individually superior, but they weren't expecting a fight, are few in number, and the planet itself isn't exactly freindly towards them.

And... que fighting!