We all have our opinions about this.
The question was:
Do I need meta gaming knowledge (= about how TIM evolves in ME 3) to refuse TIM's wish?
In other words: Is everyone who destroyed the base WITHOUT knowing the story of ME 3 at least a simple hearted do-gooder?
Or are there enough hints during ME 1 and 2 to justify a decision against TIM?
yes 
We all have our opinions about this.
The question was:
Do I need meta gaming knowledge (= about how TIM evolves in ME 3) to refuse TIM's wish?
In other words: Is everyone who destroyed the base WITHOUT knowing the story of ME 3 at least a simple hearted do-gooder?
Or are there enough hints during ME 1 and 2 to justify a decision against TIM?
That's a question you have to answer for yourself.
I never bought TIM as a benevolent guardian of humanity for a moment. Others saw him differently.
All I can say is, in the end, the choice doesn't really matter.
We all have our opinions about this.
The question was:
Do I need meta gaming knowledge (= about how TIM evolves in ME 3) to refuse TIM's wish?
In other words: Is everyone who destroyed the base WITHOUT knowing the story of ME 3 at least a simple hearted do-gooder?
Or are there enough hints during ME 1 and 2 to justify a decision against TIM?
I'd say the second. TIM lies you in the face twice, once even setting you up for a Collector ambush - all to get the tech at the base. He is willing to sacrifice a colony just to get that technology. Now, it's up to your Shepard to decide whether to give him that tech or not.
In all my games I decided like I imagined to decide in real life (RL) ... although I have to admit, in RL it was rather rare for me to save the galaxy
TIM betrayed Shep, he lied to her and Cerberus' image was still not the best. What would I do with a person in RL who treated me like this?
I have another question, concerning the indoctrination.
We have seen "reaper indoctrination machines" (or however it is called in English). Their purpose is clear.
But then I heard often, that even the contact with reaper-tech or only parts of a destroyed reaper (like the one on Tuchanka) are capable to indoctrinate people.
Was there a bit more detailed explanation about the way it works?
Simple questions:
Someone touches a part of a destroyed reaper. Indoctrinated?
If a simple touch is not enough, how long must someone be near such a part? In one conversation Shep says to TIM "...you certainly were too long near the enemy..."
I guess, you see what I mean. Opinions?
If you took it as a real life thing, would you even work for Cerberus at all?
I believe it takes a short time to subtly change the character. In Mass Effect: Revelation:
The longer time is spent near the Reaper artifact the more is that change, culminating in being implanted with Reaper nanites that make further struggle impossible (only ended by killing yourself).
I think that not every part of Reaper technology can indoctrinate people. Only parts that can transmit or receive centralized Reaper signal
In all my games I decided like I imagined to decide in real life (RL) ... although I have to admit, in RL it was rather rare for me to save the galaxy
TIM betrayed Shep, he lied to her and Cerberus' image was still not the best. What would I do with a person in RL who treated me like this?
I have another question, concerning the indoctrination.
We have seen "reaper indoctrination machines" (or however it is called in English). Their purpose is clear.
But then I heard often, that even the contact with reaper-tech or only parts of a destroyed reaper (like the one on Tuchanka) are capable to indoctrinate people.
Was there a bit more detailed explanation about the way it works?
Simple questions:
Someone touches a part of a destroyed reaper. Indoctrinated?
If a simple touch is not enough, how long must someone be near such a part? In one conversation Shep says to TIM "...you certainly were too long near the enemy..."
I guess, you see what I mean. Opinions?
It's never shown just what parts of a Reaper are capable of indoctrinating people. The Derelict Reaper indocrinated the entire Cerberus team on it. There's a couple of side missions involving colonists getting indoctrinated by nothing more than dragon's teeth. Object Rho managed to indoctrinate Kenson and her team (though Shepard spent two full days in close proximity to it with no ill effect)
So what can indoctrinate people: Whatever the Plot says can indoctrinate them
How long does it take? Speed of Plot
Or are there enough hints during ME 1 and 2 to justify a decision against TIM?
I would say so. With all the rogue cells, experiments that go wrong and kill all their guys, logo placement, and poor information security the guy is terrible at running a covert organization. His plan to take on the Collectors banks on the Collectors being similarly incompetent (which, to be fair, turns out they are). Also, quite a few of his actions leading up to the Collector base are questionable (he didn't say the ship was a trap because Shepard might have given it away?!?!). And finally the game acts as if giving the base to TIM is indeed a 'bad' decision; the pragmatic Mordin and pro-Cerberus Miranda along with the entire rest of the crew question Shepard's decision.
I'm not quite sure what direction BioWare was going with TIM in ME2. I think the intention was to make him an intelligent, ruthless pragmatic which is great. The problem is all the little (and sometimes not so little) contrivances that surround the ME2 plot which heavily involves Cerberus makes him look like a drunk shut-in who's recklessness and short-sidedness greatly exceeds any limited intellectual capabilities he may have. Turns out in ME3, this might have been the case.
If you took it as a real life thing, would you even work for Cerberus at all?
Actually, I've asked myself this question again and again.
First of all, I'm indebted to them. Here begins the first conflict of interests. As far as I could know at this time, they saved me, mended me together and gave me literally a second life. I think, I would at least listen to TIM's proposals.
Maybe I would plan to get out of their claws ASAP. Therefore my first trip goes to the Citadel, where I will reveal Cerberus' plans, report about the Collectors etc.
But now I find - again - a royally ignorant Council, the never-listening Udina and a powerless Anderson.
So, what would I do? Trying to make the best out of a deadlocked situation, trading cholera for pestilence and agree to work for / with TIM, always trying to persuade myself, that they work for me.
Actually, I've asked myself this question again and again.
First of all, I'm indebted to them. Here begins the first conflict of interests. As far as I could know at this time, they saved me, mended me together and gave me literally a second life. I think, I would at least listen to TIM's proposals.
Maybe I would plan to get out of their claws ASAP. Therefore my first trip goes to the Citadel, where I will reveal Cerberus' plans, report about the Collectors etc.
But now I find - again - a royally ignorant Council, the never-listening Udina and a powerless Anderson.
So, what would I do? Trying to make the best out of a deadlocked situation, trading cholera for pestilence and agree to work for / with TIM, always trying to persuade myself, that they work for me.
I think basically, the plot of the games should have gone ME2>ME>ME3, obviously with edits to make the fact that Shepard is Alliance make more sense. I just think that a more natural progression in scale would have done wonders, plus the fact that it was a more character driven game could have cut down on some of the info dumps.
Better yet, why not have had the choice to work for either Cerberus or the Alliance from the get go. Make Cerberus the black-ops, breakaway part of the Alliance it was originally written to be and then have Shepard promoted to Spectre from there. The only thing that changes is you get your missions from TIM (or Miranda even) instead of Hackett and Anderson. To justify shooting Cerberus mooks, just have them be presented as you doing "clean-up" on failed cells.
I wouldn't really feel as though I'm indebted to anyone who brought me back to life. After all, if I was already dead, then everything's already over. It's like being grateful for being born.
I think I would be more suspicious than anything.
There is one assignment of Cerberus in ME 2: Rescue a Cerberus agent. When Shep arrives, the agent is dead and Shep can decide, how to handle the data.
1) give it to Cerberus 2) give it to the Alliance 3) keep it
Now, if there had been an opportunity to give the Collector's base to Hacket aka Alliance, I would have done so.
But how could I ever consider to give it to TIM? I didn't need any sort of metagaming to decide against this way.
Alone the facts of ME 1 (unethical experiments etc.) and what we have seen in ME 2 (like luring the Collectors to a human colony, hazarding the consequences of a total loss of the population) are sufficient for me to give TIM nothing.
I realize that there might have been valuable techs, but the risk to give these techs into the hands of a fanatic lunatic is outweighs everything, IMO.
BTW, Shep could take the base with a handful of people. Who says, that the Reapers won't try to get the base back?
That mission - interesting mission - the data? It would take EDI two years to decode it. Too bad the reapers are coming in a year. Give it to the alliance and they throw you in prison for working for Cerberus. Give it to Cerberus and you get a nice letter.
But none of what you do really matters. Keep the base and TIM is happy and you get thrown in prison. Blow up the base and TIM is mad but gets through the relay anyway and gets the tech to build his army of doom. You get thrown in prison anyway.
So here's what I figure - You're with Cerberus! Act like it! You know the risks.
Ok, if we take the plot into consideration, many events are at least questionable.
But what did you feel and / or see, when you were confronted the first time with certain decisions, without knowing the outcome?
Although I was VERY distrustful when talking to TIM the first time, I couldn't tell offhand, if he is "evil" or just pragmatic.
I wasn't sure either at first. It was easy to accept that the council and the alliance had their heads buried in the sand when it came to the colony abductions.
At the same time, shep is still an alliance soldier, and a spectre, and the savior of the citadel. I wanted to believe that if she came calling this time, the council would at least hear her out. However, she's also been dead for two years, and is now working for known 'terrorists'.
So, it wasn't until TIM said, "I don't want them getting in our way," about the alliance helping on Horizon, that I realized he had ulterior motives. So I stopped taking things at face value.... but I couldn't wait to find out what it was that TIM wanted. 
I just get around it by saying at every oppertunity I don't work for them... of which you get a lot on the game.
But still you're working for them. Game magic 
I think the Illusive Man knew he was Indoctrinated, that's why he was so insistent on bringing Shepard back exactly as they had been. He couldn't openly resist the Reapers without them tightening their control. So he used a loophole, after all no-one would question why a human supremacist group would want to bring back the most well know human hero at that time.
As to the Collector base, I destroyed it on my first run through Mass Effect 2. Illusive Man had shown me twice before that he was not to be trusted, no way I was going to hand the base over to him.
So you think, that someone, who is indoctrinated KNOWS that?
@ Psychevore
That's really an issue. As I wrote, I'd be always trying to persuade myself, that they work for me.
But really, it sounds like the shop-owner, who pays protection money to the Mafia, would say "...well, I pay them, they work for me...."
So you think, that someone, who is indoctrinated KNOWS that?
I think in case of Illusive Man it's quite possible. Usually it's not, but his contact with the Reapers was unusual. I'm basing this off Evolution comic
I still don't understand how TIM and Anderson wind up on the Citadel at the end. The only explanation is that the Catalyst brought them there.
And there was no way for the Normandy to land on weirdo world since it was overtaken by the multicolored beam which then went on to blow out the mass relay. So about the only planet available for the Normandy to land on was Mars, unless they wanted to turn around and head back to Earth.
I still don't understand how TIM and Anderson wind up on the Citadel at the end. The only explanation is that the Catalyst brought them there.
And there was no way for the Normandy to land on weirdo world since it was overtaken by the multicolored beam which then went on to blow out the mass relay. So about the only planet available for the Normandy to land on was Mars, unless they wanted to turn around and head back to Earth.
Tim went there before it got taken by Reapers. Aderson presumably got there via the same beam as Shepard. The Cataclyst doesn't bring anyone anywhere.
I think in case of Illusive Man it's quite possible. Usually it's not, but his contact with the Reapers was unusual. I'm basing this off Evolution comic
Hmm... that's my struggle with the game's continuity.
But this would answer the question, why he was literally a cyborg in the end-scenes.
Or... did he just look like someone, who was indoctrinated for a long time and now faces his end because of the corruption the indoctrination causes over time?
Hmm... that's my struggle with the game's continuity.
But this would answer the question, why he was literally a cyborg in the end-scenes.
Or... did he just look like someone, who was indoctrinated for a long time and now faces his end because of the corruption the indoctrination causes over time?
And there was no way for the Normandy to land on weirdo world since it was overtaken by the multicolored beam which then went on to blow out the mass relay. So about the only planet available for the Normandy to land on was Mars, unless they wanted to turn around and head back to Earth.
Unless Normandy was already in relay transit, in which case they're already en route to another system. I've always thought that's what the scene is showing us, since otherwise they could have just moved out of the way of the beam, right?
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