There's probably not a better modern space opera than the Mass Effect games, which is what makes its wildly incoherent plot all the more bizarre. Replaying the first title, it's hard to miss that the way that it eventually gets undercut by everything in the third. I can't decide which one looks better in hindsight — Mass Effect 1 is less ambitious (and not nearly as good mechanically), while 3 is ultimately lazier and, I think, more dishonest — but I think it does point out a really interesting problem in the way that Bioware builds their big, tentpole franchises.
Let's recap: in the first chapter, Commander Shepard (that's you) stumbles across a galactic double-agent named Saren while on a rescue mission, and is given carte blanche to hunt the traitor down. Eventually, it's revealed that Saren is working for a giant murderbot right out of central casting, and their plan is to open a gateway that lets all the other murderbots into this universe from whatever pocket dimension they've been hiding in. But surprise! the gateway is actually the ancient space station that galactic civilization picked as its center of government (living in Seattle after that New Yorker article, I know how they feel). Lots of stuff explodes.
By the time Mass Effect 3 rolls around, it would make sense for people to have thought, geez, maybe living on a massive, prehistoric portal to robot doom-town might not be a good idea. You'd think that, but you'd be wrong. In fact, during the plot of the final game, not only are people still living on the Citadel, but Shepard finds out that it doubles as the power source for the super-weapon that will wipe out the bad guys. Handy! And by handy, I mean tremendously lazy in a narrative sense.
Truthfully, the overarching plot is the weakest parts of the Mass Effect franchise. The first game is too small to sell "epic scope" — when characters like Wrex die, they haven't been around long enough to feel important, or for many players to even realize they can be saved. The third spends too much time trying to wrap up plot threads instead of actually telling a story.
By contrast, Mass Effect 2 is a heist flick. The beginning is nonsense, as is the ending (the less said about the giant glowing skeleton boss, the better), partly because those are the pieces that connnect to the other storylines. But the middle 95% of the game is brilliant, because it mostly tosses the Reapers and their Robot Death Party out the window. Instead, you wander from planet to planet, assembling your crew and settling their debts so they can join you in the final mission. It's in these smaller stories that the writers can actually explore the universe they've built, with all its weird little corners and rivalries.
At some point, it starts to feel like the quest for spectacle is not helping Mass Effect, or Bioware games, or games in general, in much the same way that the "huge crashing object" finale is the worst part of our society's superhero movie infestation. Maybe it's a broken record to say that we need more AAA games that are more about character and less about saving the city, country, world, or galaxy. It's still true, though, and the best evidence for it is the games themselves.