So here we go again, finally found the time to sit down and revise this sucker, so all that have read it before be prepared to reread it (not really, there’s not too much new stuff in here) but those that haven’t ... Be prepared to read the biggest, most grand, convoluted wall of text ever!!!
What the EMS system could be about
The EMS rating relates directly to Shepard’s resolve and hence willpower. This is most evident in how the citadel presents new options with slightly improved outcomes as the EMS rating starts to increase. The higher the players EMS is the greater Shepard’s hope or desire to survive increases which eventually culminates to him waking up in the rubble shown in the final breath scene, which can only be unlocked with the highest EMS rating. Looking at EMS as proof of Shepard’s galactic clout it could also be instrumental in influencing the Reapers desire to indoctrinate Shepard due it being proof of his military, political and social influence on others, making him the perfect Reaper agent.

The Crucible
The crucible is supposedly a super-weapon orinally thought to be developed by the Protheans which one would imagine requires some very specific parts to function correctly, however the crucible doesn’t seem to mind if you hunt down and implement every advantageous piece or not as long as the player has a high enough EMS from promoting countless numbers of N7 special forces characters, yet the StarChild says specifically that the Crucible is what has changed him but yet his demeanor towards Shepard and the choices he presents you with are dependent on your EMS rating not the parts present in the crucible itself.
The Choices
But how would a construct suddenly present you with less or more options because of your effective military strength? How would it logically be able to determine this? Did the StarChild take a gander outside, do a quick head count, checked to see how the N7 spec op teams are doing and then based on this information decided to turn a few options off just because he felt Shep did a pretty average job of rallying the galaxy together!? Seems the crucibles construction and materials has little to no effect on these choices but rather how well Shepard did at uniting the galaxy.
The two low EMS options
Depending on if you either kept the Collector base or Destroyed it in ME2 the choice your offered when you have a low EMS is different; Either offering you Control if you’ve kept it or Destroy if you decided to give The Illusive Man’s offer the middle finger, indicating that StarChild’s first option is to offer you something that connects with your Shepard’s core beliefs. It should also be noted that with such a low EMS the StarChild treats Shepard with a certain sense of disdain which could insinuate that he doesn’t ever care about Shepard he just wants him gone one way or another and hence why he’s presented with a morally connected choice to pacify him.
Anyway, If Shepard made the choice of retaining the collector (Reaper) technology it could be argued that he’s either made a choice to try and win no matter what the cost or that he’s willing to sacrifice his morality to try and use his enemies technology to destroy them insinuating that the ends justifies the means; Regardless Shepard will be ultimately making the choice to hand ‘control’ of the base over to the illusive man. It should be noted that because the collector base is of Reaper design that it is more than likely going to indoctrinate anyone who is in contact with it as demonstrated with the derelict reaper and object rho in ME2. The only physical difference keeping the collector base makes to the Crucible porject is that instead of having the Reaper heart installed, the Reaper brain is discovered in Cronos station in its place.
It’s interesting to see that what was once considered a renegade action now leads to the “paragon-colored” conclusion to the series, Indicating that Shepard’s perception (or rather the players perception) of what is right and wrong has now been clouded by the Reapers indoctrination which the codex points out to be one of their methods, this could also be why he doesn’t actually see this option for what it really is. This also raises another issue, which is “why would Shepard actually care if it was blue, red, purple, tangerine or pink with plaid stripes?” the simple answer is: Shepard wouldn’t, the blue paragon and red renegade options are a game mechanic that only us the player are a witnesses too, it’s a system for us to judge quickly and easily what those options outcomes are going to be. So if we separate the colors out of the equation, we could look at it from the point of view that Shepard had already once sided with the illusive man (an agent of the reapers) and potentially could see the value in the dangled carrot of power that is the “control ending”, not only this but Shepard also showed he was able to help secure one of the most crucial bits of tech in the universe and that he was willing to sacrifice humanities soul to do so, proving that he was malleable and more willing to see things from the enemies perspective, not only making him easier to indoctrinate but that he had enough clout to keep around as an asset due to his outcome focussed attitude. This might also have been the easiest way for the reapers to get Shepard out of the picture and remove him as a liability in their war against organics.
This could be paralleled with the alternative low EMS option of Destroy being the only option, demonstrating Shepard’s desire to overcome the Reapers but never actually having the strength to do so. Either way the Reapers win their psychological battle with Shepard and in both cases plays to Shepard’s weaknesses to take him out of the picture one way or another depending on his stance. This could possibly just be demonstrating their desire to take the path of least resistance when dealing with Shepard.
When does reality become fantasy?
Now, if we chose to believe that everything from Harbingers beam onward is just happening in Shepard’s head and that he’s actually heading down the slippery slopes of indoctrination, than we can assume that everything that takes places in the citadel onwards; from the arguments with Anderson and TIM to the choices Shepard can make, are just illusionary fictions. Some may argue that the full blown hallucination takes place earlier in the game, possible during the shuttle crash before the hades cannon or even the glossed over APC crash just before the beam run itself. Regardless the idea of Shepard somehow surviving the citadel explosion based on a face value ending is about as believe as, well this:

A different interpretation of EMS
Now for arguments sake lets stop thinking of EMS as Effective Military Strength and start thinking of it as Shepard’s willpower and to help illustrate this point I will break down each level.
With a Destroyed Collector Base from ME2 (as I’ve already discussed the result of keeping it)
0-1749
So with the lowest EMS Shepard can only choose one option. If you destroyed the collector base in ME2 the default option will be to destroy the reapers. Not only this, but the StarChild treats Shepard with more indifference than usual. So why the one option? and why is it based on the end choice from ME2? Simply put the Reapers feel that Shepard has no worth, influence or value. He couldn’t rally the galaxy to defend earth and hence his death or indoctrination doesn’t carry a consequence for them. Essentially they just don’t give a frak about him either way and although Shepard’s resolve is high, his will power is too low, even Shepard knows he hasn’t done a very good job and knows that defeat is imminent and despite take this option he doesn’t have the strength to survive the journey back from indoctrination.
1750-2049
The Reapers treat Shepard a little more seriously this time. He might not have rallied the Galaxy to the full potential he could have, but he was still more successful than before. The Reapers now offer him an additional choice: Control (become indoctrinated) because as a servant to the Reaper cause; Shepard could now potentially influence the amassed galaxy forces to secure a quick and efficient victory for the Reapers.
Notes:
The the two handles Shepard holds in the control option are labeled BadEnding in the game design map.
Shepard’s eyes not only glow bright blue in the control ending but his iris’ also have identical patterns to those of the illusive man.
Codex clearly states that the Reapers chose to indoctrinate those in key positions of power and influence, Who fits this bill better than Commander Shepard? Considering their past candidates for indoctrinated agents.
Desolas Arterius was a high-ranked Turian general famous for his work during the first contact war.
Jack Harper (aka TIM) is possibly the most powerful human in the whole galaxy.
Saren Arterius was one of the finest Spectre of his time and carried incredible clout with both the Turian military and the citadel council.
Dr. Shu Qian was the project leader on Sidon who were developing Artificial intelligence systems for the Alliance.
Edan Had’dah was a powerful and incredibly rich Batarian aristocrat and skilled negotiator
Matriarch Benezia was a much revered and respected Asari matriarch and spiritual leader among her people.
Commander Shepard: is the first human spectre, was instrumental in stopping sovereigns attack on the citadel, stopped the collector threat, prevented the Reapers from using the alpha relay and possibly amassed the greatest united fleet in the galaxy through diplomacy and acts of valor, essentially making him the most famous and influential person of his time.
2050-2799
These present increasingly better versions of the above two options, each improvement representing both Shepard’s increase in will power (Destroy option) or the Reaper’s desire for Shepard as an asset (Control option) hence why he starts to envision better outcomes due to the Reaper’s trying to solidify their hold on him or Shepard being closer to breaking free of the indoctrination process.
The notable improvements happen at these stages.
2050 - Earth is only ravaged and the Normandy crew now survives in Destroy ending.
2350 - Earth now survives opposed to being ravaged in the control ending
2650 - Earth now survives opposed to being ravaged in the destroy ending
2800 - 3999
Shepard by this stage has proven how valuable he really is as an asset to the Reapers, not only this but by this stage the Reapers realize how powerful Shepard’s will is becoming and hence they fear he might break free of the indoctrination process, not only this they now will be facing an even large threat in the form of galactic fleet Shepard helped secure and might require a trump card to bring the war squarely back into their favor.
Fearful of loosing their best potential asset, the Reapers pull out their big guns and present another tempting choice: The synthesis of Organics and Synthetics. This choice is not only the moral high-ground but also seems incredibly amazing due to implications it has of galactic peace for both Synthetics and Organics for all eternity and essentially ends the cycle and removes the need of the Reapers. It represents the hope of a permanent end to the cycle of destruction and the dawn of the next evolutionary step for galactic life. To bad it’s a big fat lie.
Pause and think about what Synthesis and final evolution is to the Reapers; well to be honest it's more Reapers. Think about Sovereign’s conversation with Shepard or any of the taunts Harbinger gives you in ME2, both reapers state that "they are our destiny, they are the final evolution". Also take note that during the suicide mission EDI points out that the human reaper was both made from organic and non-organic materials, which would be the very definition of Synthesis from a Reaper's perspective.
This added choice is also the Reapers attempt to get Shepard to see things their way, just as they did with Jack Harper and Saren. Indoctrination isn't about being told what to do or being controlled, it's more subtle than that, it's design is more like inception in that it makes the individual full heartedly believe that the Reapers are to be revered, and that the individual came to this conclusion themselves, this creates the distinction of the control they have of the husks and the conviction of their indoctrinated mouth pieces such as Saren. Indoctrination is to truly believe that whatever thought they've planted in your head is your own.
What about Synthesis being the last additional choice as far as being a game mechanic?, aren’t ‘we’ as players expected to be rewarded for more work and accomplishments? Well, yes we are!, We’ve been conditioned time and time again for this to be the case! So wouldn’t it stand to reason that if BioWare wanted to indoctrinate “us the player” that they would use a game mechanic and typical reward system as their last best chance to throw us off the right path?
Notes: When picking this option Shepard seems to morph into an almost husk like appearance complete with glowing blue eyes which also share the same iris pattern as the Illusive man.
4000 (or 5000)
The only notable difference with an EMS of 4000+ is that Shepard now survives after the Destroy ending. Hence alluding to the fact that his will power is now strong enough to overcome the indoctrination process.
Also, this threshold is knocked up to 5000 if Anderson doesn’t survive his encounter with TIM, once again proving how EMS is directly related to Shepard’s will to survive. After all, what would distress Shepard’s mental state further? Seeing the execution of his best friend and mentor, plunging a deeper mental wound into his mind forcing him to realize that surviving this war could be a fools goal.
The indoctrination alternative
So if the events on the Crucible are real than Shepard can apparently survive coping a face full of explosion (about 1,000,000,000 that of TNT) from the complete destruction of the crucible/catalyst/citadel, he also hurtles through the vacuum of space (without a breathing mask?), manages to avoid his circulatory system from stoping after the first 90 seconds of exposure, than also manages to propel himself at around 50,000kph (31068mph) so he only takes 13 hours to reach earths outer atmosphere and resists temperatures of up to 1480 degrees C (2700 F) to than also survive the 200 mile drop to the ground by magically coming to a slow gentle stop in a neat little pile of rubble, and despite all this he takes a deep breath?.
Or, the events all took place in his mind, and because his will is strong enough and has the desire to keep fighting he breaks free of the indoctrination process, takes a deep breath and wakes up in the rubble of London where Harbinger’s beam struck him.
I know which I feel is more likely and sticks much more tightly to the lore of the ME universe.
Here’s a detailed breakdown of why this shouldn’t be possible in a face value explanation:
Supernovas
Produces the same destructive power of 10^162 Gigaton of TNT
The full strength of the blast has a range of 10au depending on the size of the star, but the remnant shockwave and radiation has a travel distance of around 50au with dissipating intensity over distance.
The Sol System Relay
The Sol Relay approximately is 39au from our star.
The Mu Relay
It was estimated that the Mu Relay was much closer to the star that went supernova (possibly as close at 13au based on in-game star charts) but just to be lenient to naysayers lets say it was still 39au from the blast center.
Due to It’s distance from the blast center it was hit with approximately only 10 Gigaton of TNT and as a result was not damaged but was flung out of it’s orbit. Although it could have been as high as 10^6 Gigaton.
The Citadel
As stated in Mass Effect Revelation The Citadel is made from the same materials as the Mass Relays. The presidium and each arm also contains pods that produce mass effect fields the protect the wards by keeping the outer skin separate from the rest of the structures, which protects it from intense external damage. It stands to reason the Citadel (with it’s arms closed) could also sustain external hits of a Gigaton or greater.
In essence; the Citadel would have to incur a massive internalized explosion, where it is most vulnerable. To be lenient lets place the explosion at no greater than 1 Gigaton (although could be as great as 10 Gigaton).
Kinetic Barriers
The shielding afforded by kinetic barriers protects against fast moving projectiles but they do not protect against extremes of temperature, toxins, or radiation.
Could Shepard outrun the blast?
The Presidium Is 7.6 kilometers in diameter, the explosion presented in the destruction cinematic has an estimated radius of 19 kilometers. To out run an explosion of this size the average person would need either a head start of 1 hour 11 minutes and 15 seconds to escape the blast or be capable of running at 900kph for the 1 minute and 19 seconds shown between the tube destruction and the central explosion.

The Human Body
At 537 degrees celsius (1000 Fahrenheit) the human skin catches fire.
At 982 degrees celsius (1800 Fahrenheit) human bones can turn to ash
The blast that would have destroyed the Citadel would have to produce temperatures in excess of 8,000,000 degrees celsius (14,400,032 Fahrenheit) vaporizing anyone inside the blast zone.
If Shepard is shown to be breathing on earth how did he get there?....
Well it wouldn't be by falling there, that's for sure...
If the Citadel was parked about 238,855 miles (384,000km) from Earth (using the moons orbital distance as a frame of reference) it would take Shepard at least 13+ hours to reach earths outer atmosphere if he was able to propel himself at a direct vector and at the safe orbital re-entry speed of 17,500 mph (28,163 kph). This could become problematic without an envirosuit as the human respiratory system can only last up to 90 seconds within a vacuum.

Now assuming he can survive temps of up to 11,726 degrees Celsius (21,138 fahrenheit) during the re-entry stage he would now have scrubbed off most of his speed due to air friction. He still needs to be able to survive the extreme drop to the ground. During this stage he should reach his max terminal velocity speed of 126mph (203kph) once he enters past the thermosphere, making his fall last around around 1.6 hours before the ground breaks his fall. However the air from 9 kilometers and up has an average tempt of around -35 degrees celsius causing Shepard to suffer from both Hypothermia and Hypoxia making him totally incapable of controlling his fall.
But yet we see this....



Also, here' a very in-depth rubble comparison of the ending scene done by Gunslinger_ruiz: http://social.bioware.com/forum/1/topic/355/index/9727423/2140#11951474
Other things to keep into consideration:
The illusive man (Jack Harper) was altered by a Reaper Artifact on Shanxi during the first contact war (about 3 decades before ME2) Not only did this encounter change his eyes (that’s right, they’re not implants), it also makes him able to sense Reaper artifacts and also gave him the ability to speak every alien dialect including that of the Reapers themselves. It’s also to be noted that he started Cerberus after this and that it’s possibly an idea that Reapers implanted into him... he’s also indoctrinated.
Shepard’s encounter with Object Rho is considered Canon by ME3 lead writer Mac Walters as stated in his comic ME:Conviction.

Object Rho is considered only one of the many possible points in which Shepard’s indoctrination could begin, although it’s the most obvious considering this artifact affects Shepard much in the same way the Arch Monolith affected Jack Harper (by putting him in a coma).

The illusive man is the only person (other than Reaper-Child) to consider Control as a viable option, and considering he’s indoctrinated would you really consider this to be a wise choice?
Only Saren and maybe Kai Leng consider Synthesis to be the only way forward, but yet again “Indoctrinated”
All you most trusted friends and allies (even EDI and the Geth) would consider Destroy to be the only option... and none of them are indoctrinated.
All through ME2 Harbinger wants to capture Shepard as mentioned in all of his comments to the commander, not only this but it’s shown in ME:Redemption that the Collectors want Shepard’s body. So why doesn’t the illusive man just hand Shep’s body over to them? Simple: He’s indoctrinated, not a husk, the Reapers have planted subtle ideas in his head not assumed control of him, The Illusive man still has some degree of free will and in all honesty he believes that what he is doing is right, unfortunately the Reapers have clouded his judgement.
The meaning of the word Catalyst:
Chemistry: a substance that causes or accelerates a chemical reaction without itself being affected.2. something that causes activity between two or more persons or forces without itself being affected.3. a person or thing that precipitates an event or change.4. a person whose talk, enthusiasm, or energy causes others to be more friendly, enthusiastic, or energetic.
Would BioWare even intend for Shepard to be indoctrinated during the production of ME3?
The short answer is yes. We have proof of this in the documentary app “The final hours of Mass Effect 3”.

“...The gameplay team was still experimenting with an endgame sequence where players would suddenly loose control of Shepard’s movements and fall under full Reaper control...”
So the first thing we can garner from this is that it was intended by BioWare to have Shepard indoctrinated at the end of the game, so the argument that BioWare aren’t clever enough to come up with ITD is false. Anyway, If they did intend to have Shep indoctrinated than there must have been some point in Shepard’s history that lead to his indoctrination, especially if it was full-blown enough so he’d be under complete control. This sentence also alludes to the fact that there are multiple stages of indoctrination by utilizing the adjective “full”.
“...(This sequence was ultimately dropped because the gameplay mechanic proved too troublesome to implement alongside dialogue choices.)...”
Anyone who just glances over this sentence might be lead to believe that it says “The Indoctrination of Shepard was dropped because it was too troublesome to implement” but it doesn’t say anything of the kind. All that sentence says is that the mechanic of having the game suddenly take control away from the player was dropped but not the indoctrination concept. It also says that it was hard to implement along with the dialogue choices, but it never says that the related dialogue choices were ever removed and hence we are still presented them in the game during the end sequence. The sentence never once mentions that Shepard being indoctrinated was dropped, just that one physical gameplay component related to it was.