Many of us -- myself included -- assumed for some time that the Others were the remains of Dharma, and it's instructive to recall why. Back in Season 2, when Tom was still the bearded Mr. Friendly, he quoted "somebody a whole lot smarter than anybody here" as saying "since the dawn of our species man's been blessed with curiosity." That quote, of course, was attributed to Alvar Hanso on his Foundation's website, leading a lot of us to conclude that Mr. Friendly was a former disciple of Hanso.
It appears the foregoing was a big red herring, but appearances can deceive. Aliases, after all, are practically a theme of the show. Consider how many characters have been known by more than one name: Henry Gale/Benjamin Linus, Drs. Marvin Candle/Mark Wickmund, Sawyer/James Ford, and Kate/Maggie/Joan/Annie/Monica are the obvious examples. I believe that list of aliases will eventually grow to include Alvar/Jacob, as well. But why on earth would Hanso go to all the trouble of using different names?
One possibility is that our Magnificent Man actually had two related but distinct projects in progress on the Island. There was the Dharma Initiative devoted to influencing the core factors of the Valenzetti Equation. The Other project was a hedge on Dharma's failure. Under the alias Jacob, Hanso began recruiting exceptional people for what a poster named todell calls the Human Stash. If and when the rest of humanity was extinguished, these exceptional people would go forth and rebuild a new and better world in their own exceptional image.
Another possibility, which I'll revisit in its own thread, is that the Dharma scientists caused some calamity, necessitating counter-measures. Let's say the Island is located outside of space and time -- a kind of Panoptichron from which the past and future can be observed and changed. Perhaps, in attempting to alter humanity's fate, Dharma accidentally damaged multiple timelines, setting off a chain reaction (i.e., the Incident). Hanso recruited special individuals capable of transcending time and space as "time agents" to repair the damage.
Then there are the possibilities that take us literally and figuratively through the looking glass. What if Alvar has a whole other personality just like Hurley -- one named Jacob? Or what if Alvar has a "bad twin" named Jacob from a mirror dimension -- one with apocalyptic ambitions? I've always wondered why Alvar lacked a mustache in the photo from the Swan Orientation. Okay, that last possibility is admittedly absurd and doesn't even technically involve an alias, but I'm a sucker for mirror Spock scenarios...
However it happened, the result was two groups working side by side on the same Island, each with no knowledge of the other. Things went swimmingly until they inadvertently made contact. Through a series of misunderstandings, the two groups grew hostile. Perhaps the Others kidnapped one of the scientists, prompting the latter to retaliate by killing an Other. The conflict quickly escalated, and when Hanso tried to intervene, he was banished from the Island, possibly in the AH/MDG Incident.
With him went the truth and any hope of peaceful resolution...
