We've had some going back and forth weither a Cylon can be a Sympathizer to side with the humans to win the game. Similar to if a human gets it they side with the Cylons. 

The main reason for me thinking a Cylon can side with the humans is if he's not revealed(otherwise if he was he'd give his cards away) and at sleeper phase he gets the Sympathizer card. In the core rulebook on page 19 in the first paragraph under Sympathizer it says: 

…"The 'You Are a Sympathizer' card represents a human or Cylon who wishes to side with the other team"…

I would take that as a Cylon can get the Sympathizer card and side with the humans. 

iirc, getting a "You Are A Cylon" card means you're a cylon, even if you choose not to reveal. 

Correct, I wasn't meaning they'd turn into a human, but instead be a Cylon that sides with the human side. So you would move to the Cylon locations but would still try to help the humans win by playing positive cards and trying to get crisis cards to help them jump. 

Thematically it would be like Caprica Six who is a Cylon, lives with the Cylons but sides with the humans and tries to help them out as much as she can. It would also only work if all resources are in the Blue during sleeper phase, otherwise you go to the brig and the card turns into a "You are not a Cylon" card.

Otherwise it seems odd that they'd specifically state that in the rulebook. It could very well be an error in text and they had meant to take it out, that's why I wanted to see what others thought. 

I am not sure if I understand you fully, but I think the rules pretty clearly state that cylons only win if the humans lose, so no, the cylon cannot play sympathetically for the humans.  This is how the base game works.  The Pegasus expansion adds the possibility of having Cylon Leaders like Caprica Six with complicated agendas and sympathetic cylons that may have agendas, some of which involve the humans winning.  But otherwise, a normal Cylon player is just out and out a baddie.

I think you are not asking a game rule question but asking about this as a variant? 

I am guessing you don't have the expansions, but Cylon Leaders basically have this. 

Cylon leaders get agenda's that may favor either side.  If they are pro-human, they could be revealed and working the cylon locations with the agenda of helping humans. 

They also can replace the sympathiser as a mid-game card. 

I do have the expansions and was asking if that is how the sympathiszer works normally. Because the card isn't caclled Cylon Sympathizer and in the core rulebook page 19 it says …"The 'You Are a Sympathizer' card represents a human or Cylon who wishes to side with the other team"…  Which I would take as a Cylon can side with the other team.

As well, with the expansion you have the Sympathetic Cylon card, as well as agendas that let you be a Cylon but your win condition is changed so you win when humans win. So the Sympathizer can change the win condition for the type you the resources are in Blue.

You're crossing wires a little.

That rule refers to the fact that the card itself, like all the rest of the loyalty cards, tells you whether you are a cylon or a human -- in this case reversed. So if:

1. The resources are all blue you are a cylon (thematically only) who has sided with the humans (mechnically you're a human… or in other words you win with the humans. Later, in the Pegasus expansion, this same sort of idea was expanded to the cylon leader.) That's why you end up in the brig.

2. Any resources are in the red you are a human (thematically only) who has sided with the cylons (mechnically you're a cylon… or in other words you win with the cylons). That's why you end up in the cylon locations, but do not have a super crisis and cannot active cylon ships.