Mass Effect has to be one of my best games so far on the PlayStation console. I started off with Mass Effect 3 at first, then went back to Play Both 1 & 2 to understand in full depth the storyline for myself. OK to begin, This is my own opinion on how the Ending happened on ME3. Some critics talked about Indoctrination as the ending, some hated the ending while some liked the Extended Cut DLC ending. To all this fact I noticed a strange thing that happened on ME2 that I think people have been missing out. For one thing when Shepard and his crew entered the Ship that contained the Reaper IFF, the Cerberus crew that died there and from analysis gotten from logs were complaining about thought coming into their heads which were not theirs.

Evidence 1

From a specific Log which Shepard encountered, it played a video about crew members remembering the same incident, which logically is not possible. Now if Indoctrination started is because they have been exposed to the Reaper signals that have been on the Reaper Ship that the Cerberus crew were investigating.

Evidence 2

Shepard’s crew got away from the ship with a Geth called Legion. Now if Indoctrination is accurate, the Geth should have been corrupted while on board the Reaper ship because it was in fact a Synthetic which mean its more easier to displace their logic.

Conversation between Legion & Shepard on ME2
When Shepard asked Legion how come he’s different from other Geth he has been fighting (i.e.to be specific) how come Legion doesn’t open fire on Organics. Legion replied that He is in fact a consensus of many Geth running up-to 1144 (illustration) Geth programs simultaneously that in fact there are many Geths in him. And that he came to investigate the Old Machines referring to the Reapers. The Legion said that the Heretic conforms with the Old Machines ideology and he explained the difference why they can do that. That if their program runs a logic of (using: illustration) 0.32421 and the Heretic (i.e which are Geth that has accepted to the Reapers Indoctrination) runs a program of 0.32422, that the difference in number can easily displace a Geth in believing commands from the Reapers.

Now coming back to our Evidence 2 while the Geth was present at the Reaper IFF, don’t you think Indoctrination would have been possible? In-fact I believe, This was the starting point of Indoctrination that affected both Shepard and the Geth called Legion.
As Legion said Heretics are also Geths that have accepted Reaper indoctrination, and I believe out of the 1144 programs running on the Geth a majority of it’s consensus reach a logically conclusion that the Old Machine will In-fact save them rather than destroy them. which will explain how Legion was caught in ME3 and attached to a Reaper Signal device on a Geth Dreadnaught broadcasting Reaper Signal to other Geths to fight the Quarians.

Evidence 3
After Shepard destroyed the Prototype human-Reaper when him and his crew entered the Omega 4 Relay, the Reaper told him that failure is inevitable and eventually Shepard will be under their control. To all fact finding, I believe this is where their Indoctrination was influenced on Shepard. In the beginning of ME3 Shepard saw a boy running into the ventilation duct that he tried to save, when Anderson called him, there was nobody there. Even when Shepard was escaping on the Normandy, he still saw this little boy entering into the Alliance shuttle off which no other military personnel seem to see this same boy before the Reapers destroyed the Shuttle. Still anytime Shepard Sleeps he dreams about himself saving this boy and the Reapers coming specifically for this boy and a voice plays in the background (i.e. if you listened closely) “SERVE US”.
This will in-fact be a sign of Indoctrination manifesting itself. If you remember when Shepard removed the head gear of the Cerberus trooper on Mars, their face shows a sign of Indoctrination which was done by the Illusive man because he was experimenting on Indoctrination. This also goes to question the fact that the Illusive man was indeed Indoctrinated but didn’t manifest fully. which mean it was coming to him slowly.

Evidence 4
At the final battle when Shepard and the Alliance team were racing to enter the beam to the Citadel. Harbinger’s laser didn’t touch Shepard but grazed near and passed him which resulted in the destruction of his armor. Now I believe from this point Shepard fell into a deep coma and what we saw after he woke up was in-fact a process of thought that was coming through his mind. The Reapers couldn’t Indoctrinate Shepard fully because his will is just too strong to comply plus, his body is partly synthetic due to the Lazarus project which makes the Indoctrination process difficult because Indoctrination is done on Organics or Synthetics not a combination of both.

Therefore I believe that what ever ending we saw whether it was the “Control”, “Synthesis”, “Destroy” or “Refusal” ending all are just a basis of what was going on in Shepard’s state of mind while he’s in some sort of Coma. Which means the battle against the Reaper is still going on. From the Logs gotten from Liara T’soni the Protheans fought the Reapers for nearly a Century before they were completely wiped out. which means that the Galaxy has about the same time frame before the Reaper will eventually defeat them, of which the Crucible is the only device that is capable of defeating a Reaper because conventional ways won’t work. If Shepard is in a coma and didn’t enter the beam to open up the Citadel which means, the crucible is still in deep space and Admiral Hackett hasn’t arrive to the battle scene. Which also means now either Admiral Anderson has to send an Infiltrator team to explore the Citadel to Open it up for the Crucible to be attached to it which will eventually destroy the Reaper because the crucible has one function, to terminate the Reaper with a power blast.

In all, I think we haven’t seen the last of Shepard remember this is 2186 CE which means it just only 6 months after Shepard destroyed the Collector base did the Reapers attack Earth and other Galactic Nations. So there’s more to the Story than what we already Know. The Leviathan DLC even explains the origin of the Reapers and proves that the Leviathans are actually the creators of the Reapers so therefore they can control the Reapers. Which mean this war is only just beginning and the Illusive man is still out there finding ways to Control the Reaper if in-fact he hasn’t already found a way.