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In ME1 Shepard's pursuing Saren. Saren's not a generic powerful bad guy; he's specifically a Spectre who's gone off the rails, abused the powers of the title, and either been brainwashed into or voluntarily started working for the bad guys, while claiming secret knowledge that justifies him. You can easily read Shepard (especially a Ruthless or more renegade one) as partly motivated by the consciousness that they could become Saren and have a deep need not to.

Then in ME2 ... Shepard wakes up to find they've been saved from death by extremely sketchy people wielding equally sketchy technology (like Saren was), that they are being offered a deal to work with the bad guys (like Saren was), and decides, based on evidence almost nobody else believes, that working for the bad guys is currently the right thing to do (like Saren did). ME2 is the process of Shepard working out who they are again and exploring how far they are or aren't willing to go in Not Becoming That Guy.

(Meanwhile, in the background, the Illusive Man - unimaginably well resourced, master manipulator, galactic éminence grise, is having his own "that guy is doing to me what I specialise in doing to other people, but he's better at it" envy-crisis about the Reapers.)

In ME3, Shepard has four different antagonists:

* the actual Reapers, unstoppable killing machines who will happily erase large swathes of galactic life in pursuit of their own interests;

* the Illusive Man, who has concluded that the only thing wrong with the galaxy-ruling indoctrination swarm is that he/humanity isn't in charge of it;

* Kai Leng, a disgraced N7 with strong Main Character energy, who does to Shepard exactly what Shepard does to NPCs (turns up, grandstands, derails everything, is exasperatingly impossible to kill);

* the clone, who in this construction is really just the logical conclusion of Shepard having to fight various different refractions of themself.

Kai Leng and the clone are human-level, obvious parallels to other life choices Shepard could have made; while in attempting to simultaneously fight the Reapers and the Illusive Man Shepard is forced into choice after choice reminding them that this could be you (how many people are you willing to kill? How many people are you willing to manipulate?), culminating in the red and blue endings.