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"He was the final boss. But you just don't understand how serious this was. This isn't some random Marauder that popped out of nowhere. All this time, he waited for you [...] His name was Marauder Shields"
Affectionate Parody: The comic as a whole alternates between this and a more venomous critique of Mass Effect 3's endings, mostly at the beginnings. Slogans supporting the controversial "Retake Mass Effect (3) movement" appear at the bottom of the first few episodes of the webcomic, subsequently replaced with the comic's own tagline "Hope is Alive".
Deus ex Machina: In terms of the webcomic's alternate continuity, the titular character qualifies—he comes out of nowhere to "save" Shepard.
Hero Antagonist: Either Shepard (Marauder has the utmost respect for Shepard and wants to save him, but Shepard doesn't know this) or Shields (he's trying to save Shepard from the endings the only way he can), depending on which angle you want to view the series from.
Interrupted Suicide: Aria T'Loak in Episode 13 ("The Queen") takes a gun to her head to avoid being reaperized and end her life on her own terms. She is interrupted by none other than Commander Bailey.
Killed Off for Real: Jack's students, incinerated just in front of her, with their white bones barely visible in the fire.
Put on a Bus: Commander Shepard. This is presumed, as the story barely arrived at its half-season finale.
Retcon: In the final mission of Mass Effect 3, the Reapers will stop at nothing in their attempt to kill Shepard. In the webcomic, the Reapers suddenly seek to use Shepard, despite the webcomic beginning with Shepard nearly being killed by Harbinger.
The controversial Catalyst, and everything associated with it, was removed from the story or completely reworked so that Marauder Shields' story could be explored.
This includes the history of the Leviathans, the ancient apex race that created the Catalyst. Their story was revealed in the Leviathan DLC, which was released after the start of the Marauder Shields series. Since it is so closely tied to the Catalyst, it is irreconcilable with the webcomic. It is also easy to put aside without significantly altering the main plot of the game.
Re Write: The author has stated that he's trying to avoid these in favor of revisions. Not all agree that this is the case; however, the author does try to build on canon events such as the beacon on Eden Prime.
The Reveal: In Episode #6 ("The True Catalyst"), Marauder Shields' true identity was revealed to be Nihlus Kryik, the turian spectre from the first game who endorsed Shepard as a Spectre candidate before being killed by Saren on Eden Prime. Nihlus' body has been taken from Eden Prime and reaperized by the geth servants of Saren Arterius - with whom Nihlus was emotionally attached in the official canon - which is explained by emphasizing Saren's insanity and showcased as his last semi-awake stand before succumbing to total indoctrination (mirroring the events involving Matriarch Benezia on Noveria). A group of marauders has been hidden in the Citadel's core during the events of the first Mass Effect game, awaiting the arrival of the Reapers, which explains Nihlus' presence at the beam during the events of Mass Effect 3.
In Episodes #10 ("Spectres") & #13 ("The Queen"), Commander Bailey can be seen sporting a sexy eye-patch, resembling the one worn by one Saul Tigh, who was played by the same actor as Bailey (Michael Hogan).
In #13 ("The Queen"), one Christopher Blair can be seen discussing the Reaper attack taking place in Episode #12 ("Breaking Point").
In #16 ("Brothers Till The End"), James tells Javik the reason he became The Nicknamer was because he once called his girlfriend Sarah when her real name was Yvonnenote reference Yvonne Strahovski, who played Sarah Walker on Chuck and Miranda Lawson in Mass Effect 2 and 3.
In #23 ("Dominoes Will Fall"), the Virmire Survivor is leading Special Task Force 343. The Codex entry at the end of the comic also references a special shock trooper program known as the Helljumper project.
In #24 ("Never Alone") the codex entry mentions that the Alliance tried to copy the design of an Asari super-computer network, giving it the codename Project Durandal.
Took a Level in Badass: All of Shepard's squadmates, current and former, supporting characters, and even one-time side-quest characters step up to the plate with Shepard out of action. Especially when compared with Mass Effect 3.
True Companions: all of Normandy's crew and the Normandy (EDI) herself. No one abandons Shepard, they all fight for him/her and for each other.
Kasumi (Episode #23): "They're coming for you... I know they are. We would never leave you behind. just hang in there Shep... Wherever you are."
Unstoppable Rage: Jack starts hurling around and tearing apart husks and cannibals like a one-woman biotic hurricane. She even did a Biotic Charge from the face of Big Ben straight into a Sovereign-class dreadnought, most likely planning to tear it apart from the inside.
Watching Troy Burn: couple of panels show the burning London with giant Reapers circling above it.