The ecological succession that creates a deciduous forest starts with the greed of pines. Fast-growing conifers colonize a suitable area and take it over, suppressing ground-cover growth with their light-blocking needles. As the pine growth becomes more dense, this advantage backfires. The lower branches of the old trees die, and infant pines starve in the darkness beneath that crowded sky.
This is a fitting allegory for the universe of Mass Effect, where humanity emerges into a galaxy run by entrenched powers uninterested in assisting them. Early on, Mass Effect establishes that the Citadel Council forced humanity to establish colonies in dangerous parts of the galaxy, then refused to offer aid when those colonies were inevitably attacked. The existing power structure is only interested in humanity's ability to serve as a buffer against its enemies, not in helping us thrive.
Despite all this, humans get a comparatively sweet deal. After the events of the first game, they take a position on the Council and get to play a role in decisions that affect them. The Elcor, Volus, and Hanar are not so lucky. Although they have been taking part in galactic politics for centuries by the time humanity first contacts an alien species, these races are denied any real representation. Little stands between them and the fate of the Batarians, who angrily cut ties with the Citadel after the Council gave humanity colonization rights in sectors the Batarians wanted for their own.
Whatever complaints these races have with the galaxy as it is, their luck could have been even worse. Fifty thousand years ago, the Protheans were more advanced than galactic civilization is at the time of Mass Effect. Had they been allowed to flourish, they would have been a power so dominant that any challenge from the races of Shepard's Citadel Council would have been negligible. More to the point, it would have been impossible. Many pieces of evidence from the games demonstrate that the Protheans were watching or even actively assisting the development of the humans, Asari, Hanar, and other species. Our first steps into space would have placed us right into their hands.
As the Prothean survivor Javik makes clear, those hands would not have been entirely welcoming. According to him, the Protheans offered every race a simple choice: join us or fight us. Against the might of the enormously advanced Prothean empire, only one option could realistically result in survival. The Protheans would have made slaves of the galaxy's current civilizations. Indeed, preserving a core of Prothean society to dominate the galaxy's more primitive races and transform them into an effective fighting force against the Reapers was the purpose of Javik's failed mission.
In a galaxy without the Reapers, however, even the Protheans would have been subjugated. The 50,000-year cycle of galactic flourishing and extinction has been repeated countless times, creating a chain of cultivation reaching back tens of millions of years. If humanity could not even assert itself against species that had a head start of only thousands of years, how would it fare against galactic civilizations that had been around for eons?
Would humanity have even developed in such conditions? Garden worlds are one of the galaxy's most precious resources, after all. With millions of years to search, certainly some advanced race would have eventually found Earth and decided to settle there. It took us only tens of thousands of years to expand into every almost every corner of our world; an advanced alien race could probably reach the planet's resource capacity in just a few hundred years.
Could human beings have evolved in such an environment? Would they have been allowed to?
Genocide is, after all, a fact of galactic life. The Rachni attempted to exterminate the Asari and Salarians. In response, the Salarians uplifted the Krogan and used them to kill off the Rachni. Once the Krogan became unruly, the existing powers recruited the Turians to help them suppress their one-time allies. When even that failed, the Salarians came up with a virus that would slowly exterminate the race that had saved them. Similarly, the Quarians gave life to the Geth, then attempted to eradicate them. By the time of Mass Effect 3, the Salarians, seemingly having learned too little from their exercise with the Krogan, are experimenting on the similarly violent and temperamental Yahg.
Humanity joins the Council at the end of the first Mass Effect game, but they do not really join the galaxy's ruling class until Mass Effect 3, when Shepard is given multiple chances to wipe whole species from the stars. She can choose to deceive the Krogan and allow their race to slowly die out. She can allow the Quarians to destroy the Geth, or vice versa. Patricia Hernandez rightly sees shades of the "white man's burden" in these choices, but they speak to an even more disturbing truth.
When Shepard speaks with the Catalyst at the end of Mass Effect 3, it explains that its plan is to harvest intelligent life, storing those civilizations in the form of Reaper ships, which will return in the next cycle to repeat the process. Horrifying as this sounds, Mass Effect shows us that we cannot avoid being the instruments of genocide. We will become reapers, one way or another.
We will destroy the species that threaten us, like the Rachni and the Geth. Even if we avoid that, as Shepard can, our expansion across the galaxy's garden worlds will still choke out emerging intelligences. We will trod them underfoot as we build our colonies, killing civilizations before they even form. The few species that avoid that fate and reach the stars will be subjugated, if not literally then at least economically. Unable to expand or challenge their technological superiors, these races will starve inside the crowded sky.
The Mass Effect trilogy is not a grand tragedy of inevitable conflict between organic and synthetic life. It is a tragedy of the cruelties all intelligent species inflict on one another, intentionally and otherwise. It is a story of the old suppressing the young, the uplifter suppressing the client.
Unfortunately, the ending of the Mass Effect trilogy aims at the wrong target entirely. Javik, completely dispensable for the official justification for the Reapers, ended up as DLC, and without him this theme cannot really crystallize in Mass Effect 3. The writers at BioWare ultimately chose to explain their universe using principles they'd repeatedly contradicted, rather than the theme they had built up through three games and actualized through the gameplay of cooperative storymaking.
That problem makes the Reapears a reasonable solution. Without a gardener to prune away the old races, new races will not flourish. Trapped in their home systems, subjugated, exterminated, or snuffed out before they evolve intelligence at all, their cultures will be lost. The Reapers clear away the advanced civilizations, preserving their culture in enormous synthetic intelligences, giving the more primitive species a chance to grow into the stars. That is a story that lives up to Sovereign's explanation of the Reapers' intent, and one that would pose a genuine moral challenge at the end.
We only exist because the Reaper's genocides granted us the opportunity to thrive. They were our salvation through the destruction of older races. To give new civilizations a chance to thrive, they must clear us away. Can we really choose to destroy them, knowing that by doing so we consign countless future races to death, subjugation, or nonexistence?
That's a decision I would have liked to make.