If my theory that the losties are being pulled from the alternate (plane doesn't crash) timeline into the real timeline, and they somehow appear to be infected, then I think it's smokey bringing them over.

Russeau comes to the island post "Incident." Her team becomes infected with whatever this is that Sayid now has. She shoots them before they kill her and avoids becoming infected herself. The only reason (in my mind) that they are infected in the first place, is because they died.

Claire was in a New Otherton house when it blew up. She's now infected. She probably died in that explosion and came back to life with the same thing that Sayid now has, and Russeau's team had.

They all occured after the destruction of the island in the alternate timeline, which means that they are probably being pulled from that alternate timeline, which is then an infection of their bodies. And I think smokey is doing it to them.

I'm not sure I quite grasp what you're trying to get at. If you're suggesting that Cerberus is somehow "stealing" people from the ALT timeline and inserting them into the corpses in this timeline to create pseudo-zombies, I suppose it's a possibility. However, the fact that two of these examples - namely, Claire and Sayid - aren't "missing" in the ALT timeline and seem to be perfectly fine would seem to indicate otherwise. Claire has been infected for several years. But in the ALT, she's fine all the way up to 2004. When does the snatching take place?

Sure, Claire and Sayid are fine in 2004, what we've seen of the alternate time-line so far, but we haven't seen past 2004. And since it's 2007 on the island currently, they won't be snatched for another 3 years.

I don't know... I just like the idea that the other time line is used to fill voids in the real timeline.

The idea is not so bad, actually. I'll try if I can wrap my head around it.

You're right, contrary to all appearances so far, all might not be well in the ALT timeline. Darkness might yet consume all their hearts. In the ALT, Smokey might not be trapped on the Island, but instead run rampant in the real world.

Smokey as we see him now in Flocke, is maybe the one who's been cheated, who's been banished to the Island, possibly - and that's only a very half-baked theory so far - by the creation of the ORIG timeline.

Banished Smokey is not ultimately defeated Smokey, though. He's been trying to find a loophole ever since.

Whatever that loophole is (and I have no idea how he could have pulled this off), bringing over ALT Losties might be a part of it. It would be a very good explanation for where Flocke suddenly came from. According to this theory, Flocke would be ALT John Locke, completely consumed by darkness aka Smokey. The dead body is ORIG John Locke. Both Lockes would have to be killed by Ben, in similar circumstances (or otherwise we have no explanation for Flocke's memories).

And Smokey is now looking to substitute all (or some key) Losties with infected ALT Losties.

There's a milliion problems with this neat "void filling" theory, of course! First of all, it would require all (key) Losties to die in both timelines at some point between 2004 and the present (if Smokey succeeds, that is). That might be the reason why the temple Others are suddenly so adamant to herd them all at the temple. It's not pretty to think how close Dogen came to total desaster, though, by his initial command to shoot them all.

And why should Flocke need more of the Losties, why not just escape the island as Flocke and call it a day. He's already taken care of Jacob and that's the end of it, isn't it?