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*curses the people in Wales and their "fun" games*
Yup. I'm going mad trying to figure this out.
I started listing out all the possibilities I could think of for Boe's "you are not alone" thing, stating pros and cons to each one - Time Lord(s), the Master, Rose, Companions in general, future child/children of the Doctor, long-lost child, Susan - and I realized that I think I'm tying the "you are not alone" thing too closely to the "last of his kind" thing. They may very well have nothing to do with each other. (My own little breakthrough moment there.)
Of that list I mentioned above, I think the only one you can really cross off yet is "Companions in general" because of the Doctor saying, "I don't think so. Sorry." to Martha. Or at least if Boe *was* talking about all the people the Doctor hauls along on the TARDIS, you're going to wind up with an "Uh...thanks? Not to sound ungrateful, but REALLY?" moment for him with the big reveal.
Time Lord(s) - would make the most sense in the context of the "last of his kind" thing and would make the Doctor happy and relieved he wasn't alone in that way. And they could have been doing some sort of AU hideout so the Doctor *would* have been temporarily "alone." Gallifrey would still be gone, though. And would seem *sort* of an "oh, never mind" cheat to this whole part of his character since S1, but I'm not sure why. Maybe this is just me.
The Master - we've heard he's coming, and he also could be hiding out somewhere so that the Doctor couldn't pick up on him. But you'd think that if Boe knew the Master was a Very Big Deal, he'd also know this wouldn't be a good thing and should have clued the Doctor in right away - made it more of a warning.
Rose - we've been getting some Bad Wolf and Rose stuff popping up in episodes of S3 and in Torchwood, so they *could* be clues. I think her return would make the Doctor happy down to his toes, but this would be a different kind of "not alone" than the return of the Time Lords. And do I even need to mention how much this answer would rock my socks? But I've heard way too much about BP moving on to think that there's going to be a Rose return anytime soon. Plus the Boe "secret" was supposed to be mentioned in "New Earth," which doesn't really fit very well with this answer.
Future Child/Children - Maybe the Doctor has a kid during this the-Doctor-gets-married episode? And while genetically not Gallifreyan (since I think they're going with the book that the Doctor becomes human during all this), there'd still be that connection. This would be kinda weird though, since you know by the end that the woman he marries doesn't pack up and go off traveling with the Doctor - not exactly a "you are not alone" thing to have an absent family somewhere.
(URG. Can I just say I'm dreading the angst that will come from this episode? I can *totally* picture the the end with the Doctor begging this woman to come with him, but she didn't sign up for this weird alien life or something. And so he'll have another end of TGitF-type moment, except 10x worse... WAH. *sobs* And meanwhile, RTD will be cackling to himself and plotting new ways to squish the Doctor into an angsty paste. Perhaps melting down K-9 while bagpipes play 'Amazing Grace' in the background?)
Long-Lost Son/Daughter - Instead of a future child, the Doctor has a kid he doesn't know about. Half-Gallifreyan (or quarter) since if the kid's mother was Gallifreyan, I'm sure he would have known about him/her and the child probably would have gotten caught up in the war. This certainly would take care of the "you are not alone" thing since you'd think there'd be some genetic longevity there, and a possible more permanent Companion. And there might not be this mental awareness there like how he seems to be with other Gallifreyans. However, insta-kid plots always seem very "pat" to me, and I kinda doubt this would be any exception.
Susan or Descendants of Susan - Susan's a bit of an enigma to me, since if she was still out there, you'd think the Doctor would have *not* been so adamant about being the last of his kind. Maybe she got called back to Gallifrey during the war? (Or maybe the Face of Boe *was* Susan - ha! Okay, I'm getting a bit off here...) But it seems like the Doctor would have the hugest of headsmack moments if Susan/descendants of Susan were to show up - "CRAP! That's RIGHT! GRANDDAUGHTER! *slams head against console*"
So in conclusion...I don't think I really know *what* Boe was referring to. And this will drive me barking mad for the rest of the series, with occasional fist shaking and the like.
ETA: Okay, I *completely* forgot about RTD saying that the answer would be "devastating." So the Master now gets bumped *way* the hell up on this probability list.
ETA2: Oh, forgot to mention my cracked-out theory of BadWolf!Rose becoming a sort of guardian angel. A deus ex machina they could pull out of their asses whenever they'd need to get out of a jam - something weird happens and "oh, it was just Rose back on the game station when she was all-powerful." *cough*Jack becoming immortal*cough* This *could* account for the Bad Wolf/Rose references we've seen. And in *that way* the Doctor wouldn't be alone since someone was looking out for him and Rose would be staying with him "forever." But that answer isn't "devastating" by any means. Heartbreaking, yes, since I'm sure the Doctor would much rather have Rose with him than this helping force. But I've kinda abandoned this theory, mainly because of the "devastating" comment. Although, I suppose it could be this *and* something else like the Master, which would be devastating... Eh, I'd rather have Rose back. :D
I started listing out all the possibilities I could think of for Boe's "you are not alone" thing, stating pros and cons to each one - Time Lord(s), the Master, Rose, Companions in general, future child/children of the Doctor, long-lost child, Susan - and I realized that I think I'm tying the "you are not alone" thing too closely to the "last of his kind" thing. They may very well have nothing to do with each other. (My own little breakthrough moment there.)
Of that list I mentioned above, I think the only one you can really cross off yet is "Companions in general" because of the Doctor saying, "I don't think so. Sorry." to Martha. Or at least if Boe *was* talking about all the people the Doctor hauls along on the TARDIS, you're going to wind up with an "Uh...thanks? Not to sound ungrateful, but REALLY?" moment for him with the big reveal.
Time Lord(s) - would make the most sense in the context of the "last of his kind" thing and would make the Doctor happy and relieved he wasn't alone in that way. And they could have been doing some sort of AU hideout so the Doctor *would* have been temporarily "alone." Gallifrey would still be gone, though. And would seem *sort* of an "oh, never mind" cheat to this whole part of his character since S1, but I'm not sure why. Maybe this is just me.
The Master - we've heard he's coming, and he also could be hiding out somewhere so that the Doctor couldn't pick up on him. But you'd think that if Boe knew the Master was a Very Big Deal, he'd also know this wouldn't be a good thing and should have clued the Doctor in right away - made it more of a warning.
Rose - we've been getting some Bad Wolf and Rose stuff popping up in episodes of S3 and in Torchwood, so they *could* be clues. I think her return would make the Doctor happy down to his toes, but this would be a different kind of "not alone" than the return of the Time Lords. And do I even need to mention how much this answer would rock my socks? But I've heard way too much about BP moving on to think that there's going to be a Rose return anytime soon. Plus the Boe "secret" was supposed to be mentioned in "New Earth," which doesn't really fit very well with this answer.
Future Child/Children - Maybe the Doctor has a kid during this the-Doctor-gets-married episode? And while genetically not Gallifreyan (since I think they're going with the book that the Doctor becomes human during all this), there'd still be that connection. This would be kinda weird though, since you know by the end that the woman he marries doesn't pack up and go off traveling with the Doctor - not exactly a "you are not alone" thing to have an absent family somewhere.
(URG. Can I just say I'm dreading the angst that will come from this episode? I can *totally* picture the the end with the Doctor begging this woman to come with him, but she didn't sign up for this weird alien life or something. And so he'll have another end of TGitF-type moment, except 10x worse... WAH. *sobs* And meanwhile, RTD will be cackling to himself and plotting new ways to squish the Doctor into an angsty paste. Perhaps melting down K-9 while bagpipes play 'Amazing Grace' in the background?)
Long-Lost Son/Daughter - Instead of a future child, the Doctor has a kid he doesn't know about. Half-Gallifreyan (or quarter) since if the kid's mother was Gallifreyan, I'm sure he would have known about him/her and the child probably would have gotten caught up in the war. This certainly would take care of the "you are not alone" thing since you'd think there'd be some genetic longevity there, and a possible more permanent Companion. And there might not be this mental awareness there like how he seems to be with other Gallifreyans. However, insta-kid plots always seem very "pat" to me, and I kinda doubt this would be any exception.
Susan or Descendants of Susan - Susan's a bit of an enigma to me, since if she was still out there, you'd think the Doctor would have *not* been so adamant about being the last of his kind. Maybe she got called back to Gallifrey during the war? (Or maybe the Face of Boe *was* Susan - ha! Okay, I'm getting a bit off here...) But it seems like the Doctor would have the hugest of headsmack moments if Susan/descendants of Susan were to show up - "CRAP! That's RIGHT! GRANDDAUGHTER! *slams head against console*"
So in conclusion...I don't think I really know *what* Boe was referring to. And this will drive me barking mad for the rest of the series, with occasional fist shaking and the like.
ETA: Okay, I *completely* forgot about RTD saying that the answer would be "devastating." So the Master now gets bumped *way* the hell up on this probability list.
ETA2: Oh, forgot to mention my cracked-out theory of BadWolf!Rose becoming a sort of guardian angel. A deus ex machina they could pull out of their asses whenever they'd need to get out of a jam - something weird happens and "oh, it was just Rose back on the game station when she was all-powerful." *cough*Jack becoming immortal*cough* This *could* account for the Bad Wolf/Rose references we've seen. And in *that way* the Doctor wouldn't be alone since someone was looking out for him and Rose would be staying with him "forever." But that answer isn't "devastating" by any means. Heartbreaking, yes, since I'm sure the Doctor would much rather have Rose with him than this helping force. But I've kinda abandoned this theory, mainly because of the "devastating" comment. Although, I suppose it could be this *and* something else like the Master, which would be devastating... Eh, I'd rather have Rose back. :D