Okay, as most of us know by now, in Noob's ending, they were revealed to be one in the same. However, this creates soem inconsistancies in that, both characters appeared in MK Trilogy.
Some people say that Original Sub-Zero's appearance wasn't canon, but since there was nothing to suggest that it wasn't, (He had a -slightly- different story, a way different ending, and new sprites, then he did in the previous games, unlike say, Goro and Kintaro, who I also like to think were Canon, but we'll save that debate for another day) I prefer to believe it was, and I believe I've come up with a hypothesis supporting that theory...
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Noob makes his 1st appearance in MK2, as we know. He is known to exist, but is never given an official story. It has been deduced that he was spying on orders from Shinnok.
Now, regarding MK3 (UMK3/MKT), The whole story seems to play out over a rather long period of time. I mean Kabal is 1st injured by the invasion of Kahn's extermination squads, but by the time we 1st meet him, he is already recovered and on his respirator. With all the players and times involved in the MK3 storyline, it would make sense that many enter the fray at different times, and many individual character stories, such as Kabal, support this. Raiden as well. He's said to join the earth warriors later, as he 1st tries to convince the elder gods to stop Kahn, which they refuse to do, as always, and then he joins the fight.
Even Smoke's Human form in MK3 can be taken as Canon, so long as it is placed appropriately in the "MK3 Timeline"
His story toward the beginning of the invasion is that he flees with Sub-Zero, thus accounting for his human form. He is then caught, and transformed into a cyber-warrior, thus accounting for his cyber form.
It's not like actual fights can be taken as proof, because then we'd need to account for Red Cage's and Blue Liu Kang's, every time both players select them. Both os Smoke's forms are said to be present in the MK3 timeline, and both appear in the game. What's so non-canon about that?
Well, I thought, perhaps the same applies for Noob.
Now in MKT, Noob's story is as follows...
"Noob Saibot emerges from the darkest region of reality - a region known as the Netherrealm. He belongs to a group called the Brothers of the Shadow, and worships an evil and mysterious fallen Elder God. His mission is to spy on the events taking place in the battle between the realms and report back to his enigmatic leaders."
Now what if expaning upon that thought, we take Original Sub-Zero's story...
"Thought to have been vanquished in the Shaolin tournament, Sub-Zero
mysteriously returns. It's believed this secretive member of the Lin Kuei, a
legendary clan of Chinese "ninjas", has returned to again attempt an
assassination of Shang Tsung. To do so, he must fight his way through Shao Kahn's tournament."
Now, we know from MKD that Noob can in fact morph out of his Wraith form and into a more human-esque skintone, as shown by his Main/Alt costume. Well, if his goal was to spy, then why not take up his old identity, to slip under the radar. That way he could gather 1st hand information, without revealing his true identity.
It is stated that Sub-Zero's intent in the 3rd tournament was not known. He was -believed- to be after Shang Tsung, but not known to be. So this means he had a false identity, with a perfect cover story.
Now, in their endings, we learn more...
Noob's ending states, "At first a passive observer, (At this point Still Sub-Zero with unknown intent) Noob Saibot would soon receive orders to side with the evil emperor Shao Kahn."
I conject that it is at this point, the following statement from Sub-Zero's ending, or a similar event (Since many endings are never 100% canon, but do provide clues to a character's intent), takes place...
"Upon removing his mask both the Outworld and the Earth-born warriors are shocked to discover the true identity of this warrior. A warrior who has long been missing from a previous Mortal Kombat, and one who will return in the fourth tournament." (And I'll note that it uses the term "Mortal Kombat" in the context of the games, not the actual in-game shaolin tournament, as you'll note by it's refering to the next one as the 4th, as opposed to the 11th. So no, the "MK1 was the only other MK tournament!" argument doesn't work.)
And at this point, he reveals himself as Noob Saibot, a warrior long missing (again, since 3 takes place over a long period of time) from the previous Mortal Kombat (2nd) and did in fact come back in the 4th game. After which he pledges a false allegiance to Kahn, and the rest is history.
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This solution takes in all information, and presents a logical conclusion, while creating no inconsistancies, and I truly believe this to be what happened, or at least close to what happened. (As in, perhaps he didn't really proclaim himself to be Noob to everyone, but rather, was found to be by a select few)
In any event, that's my theory. I'd have like to have gone into more detail, but I'm writing this in class, so I have to be short.
In any event, I'll be back to read your thoughts on the matter later when I get home, and I look forward to hearing and responding to them.