Unclean resources: the Collector base and Maelon's genophage data

I've had Shepard say abomination during the suicide mission and say abomination on Mars, when talking with TIM, as well

I don't consider using Maelon's data to be this big moral debate, unless used as an extension of the "Should the Genophage be cured" debate. By itself I have no issues using the data.

Whether or not to keep the Collector Base is more of a roleplaying issue than a moral one. Those humans used to make the Reaper were murdered by a cosmic force threatening life. We really do need all the information and technology we can get against them. The actual issue is "Should we give this powerful tech to Cerberus?".

I think this is what I've been trying to get across.  The ethical "debate" over whether or not the data are good to use is Mordin's (the scientist), not Shepard.  Mordin is the one that has to do the replication work to make sure the data were accurately recorded (i.e. not falsified despite Maelon having an agenda of his own and obviously being prepared to break a lot of ethics to get there).  Maelon also has to ensure that the data recorded on the Krogan population and cultural situation are accurate and current in order to make his assessment as to whether or not the krogan would take over the galaxy if cured, etc.  Shepard's role/orders are to make as strong alliances with as many species as he can and gain as much support and resources for the Crucible as he can.  Whether or not the data are "unclean" is not really Shepard's concern.

You're forgetting that I did say that Shepard was entitled to have a "visceral" reaction... making him "want to" destroy the Reaper larva (which is where I hear him saying that "This thing is an abomination."  I don't hear the same reaction out of Shepard when discussing Maelon's data with him (perhaps I'm not selecting the same lines here either).  He does have a visceral reaction to seeing the human corpse at the beginning of the run and expresses it as "another excuse to shut the thing down."  If the discussion leans towards destroying the data, Shepard does say it's tainted, so the game offers that possibility... but, as I believe you indicated, most of us don't destroy the data.  I'm sorry if you have some sort of objection to my assertion that the principles unwriting the code of scientific ethics have a lot to do with ensuring data integrity rather than just pandering to people's reactions to disgusting things or that it is irresponsible for a scientist to just move forward using data that they have reason to suspect because it was not gathered within the principles of good scientific practice and they know that the scientist who collected it had an "agenda" in doing so.

In regards to the CB, I don't interpret Miranda's line as a "betrayal" based on uncleanliness of the facility, although I can see where some people could interpret that way.  I see it as an expression of TIM betraying the original idea behind the whole mission.  They were sent there to destroy the base, not capture it for research.  What they've seen hasn't changed Shepard's mind nor Miranda's that destroying the base is what should be done.  The idea that there would be different technology there to be found was written on the wall well before they left the Milky Way.  If the TIMs intent was to research new tech, the premise of the mission would have been set out different.  What's obviously peaked TIM's interest is that they were building a Reaper (or he was lying to them about his motives all along).  There is no value in salvaging tech that's all about how to build a Reaper unless one wants to build a Reaper.  TIM is selling out his principles because he's power hungry... and that's a betrayal to Shepard AND Miranda.  She's expressing that with the "betrayal" line and Shepard is expressing that same thing with the "soul of our species" line.  Shepard knows TIM has an agenda and won't stay within the boundaries of good scientific practice.  If you select one of the options on the left, you get Shepard saying point blank to TIM - "You're completely ruthless.  The next thing I know you'll be trying to build your own Reaper."  Rather than deny it... TIM response with a "dodgey" answer about working for the best interets of humanity.  As I said in the other thread... it's a question of whether or not it is "safer" to allow bad scientists access to good data... or to just discard the data to keep it out of their hands (scorched earth question).

The Collector Base decision is perhaps the most baffling in the trilogy for me. It seems like the writers couldn't agree on what the decision actually meant. One moment it sounds like destroying the base means that you don't trust the Illusive Man to use it wisely or ethically, and the next it sounds like you're destroying it because "people died here". Mordin and Legion offer the most compelling arguments for keeping the base: the facility is just data, and studying it will ensure that the victims didn't die in vain. But after the Suicide Mission, they question your logic for keeping it, even though they had the best arguments for it. So is this a contradiction? Or did they just disagree with handing it over to the Illusive Man? It's all so frustrating.

Sorry for replying so late - this question passed me by.

No, I don't think "A House Divided" fits. "Unclean", where such a category can reasonably be seen to apply, is a very specific type of "wrong". It appeals to the perception of a state of grace that applies to an individual or a place, or the opposite thereof, being spiritually tainted. I can't see anything of that in A House Divided.

The problem in A House Divided is that the P/R allocation makes no sense. If mind-controlling someone is regarded as "Paragon", something's wrong. Either you don't think synthetics are valid life, and then the whole decision is morally irrelevant, or you do so, and then neither decision is in the "Paragon" sphere, if the other Paragon decisions you made until then are a measure of what "Paragon" means. If anything, I'd tend to think being mind-controlled is a fate worse than death.

Actually, Renegade has the most violent option almost everywhere, and I can make a case for ME3's Destroy ending as well. In this case, it's not clear what the more violent option is.

There are a few place throughout all three games where paragon and renegade choices seem "flipped" to different people... leading to numerous "why is this paragon or renegade" posts in the "Things that don't make sense thread" here and on the old BSN... but then people complain as well that the paragon/renegade system is too rigidly binary... so why wouldn't Bioware have flipped some choices around just to get us to think a little more about the individual choice being made rather than just playing along an arbitrarily paragon or renegade path?

Honestly, it doesn't bother me.  The color coding is not consistent, but it's not going away in those three games.  There is no point in continuing to try to force a reasoning to each ending into that inconsistent color-coding system.  The destroy ending is what it is... which is not fully renegade and the control ending is what it is, which is not fully paragon.  Honestly, by that point in ME3, I'm not even caring about the color coding system or the "position" on the dialogue wheel, it had become so meaningless.  Same thing really with ME2 - neither destroying nor radiating the CB is completely paragon or renegade... it's just an ending choice... and, to the best of my knowledge, regardless of P/R before that point, the player could still make either choice.  Heck, players can't even really agree on what a "renegade" Shepard really is all about - violent? pragmatic? smart-mouthed? insubordinate?

In ME:A - we've already been told that the P/R system won't be there.

Well, I could argue that Control is Renegade merely because it's not what the Alliance ordered Shepard to do and Shepard belongs, at that point in time, to the Alliance... based on this definition of Renegade: "a person who deserts and betrays an organization, country, or set of principles." (Merriam-Webster).  In addition, there is the reality that there are two clearly different versions of the Control ending to ME3 - one given if Shepard's alignment is Paragon and a different one given if Shepard's alignment is Renegade

For me to fear galactic "anarchy" is for me to fear the actual real universe. Evolution of life on earth is chaotic. And in a split second, a gamma ray burst can emit more energy than our sun does in it's entire lifetime and devastate everything in it's path for thousands of light years. There's no giant robot to rescue anyone or control this mess. And yet time goes on.

With destroy, I'm merely bringing a fictional universe more in line with this.