It's easy to ignore the codex section when you start playing a Mass Effect game. You concentrate on the shooting and romancing and flying around space completing missions, and you gloss over that one button in the menu. At some point, though, you'll want to know what the deal is with the geth, or the Citadel Council, or the genophage.
One of the things that makes the Mass Effect games special is how much detail is there waiting for you, and how much context it adds to the action. Mass Effect's history makes shooting a bunch of krogan feels like something that matters, rather than just another obstacle between you and the next mission complete screen.
Eventually you feel the urge to look deeper. And that's when you find whole histories of human space exploration and alien contact, and beyond that histories for each of the alien species and their progenitors that go back thousands of years.
There's a lot to it. And there will be spoilers.
The history of the Mass Effect universe begins some time before 1,000,000,000 BCE—dates are given in the format of CE (Common Era) and BCE (Before Common Era)—when a species called the leviathans controls the galaxy. Observing a repeating cycle in which civilizations collapse after creating synthetic lifeforms that turn on their creators, the leviathans seek to break this cycle by, ironically, creating a synthetic intelligence. They call it the Catalyst.
The Catalyst is intended to serve as a bridge between organic and artificial life, working to preserve organic species at any cost. The Catalyst, believing conflict to be inevitable, sees the best way of achieving this to be taking organic civilizations at their peak, shortly before they're responsible for their own downfalls, and absorbing their genetic material into new lifeforms that it can maintain forever. It preserves them, but only in the sense that it turns them into jam.
The Catalyst begins with its own creators, transforming them into the first reapers and beginning the war its creators had tried to avoid.
A reaper called the Leviathan of Dis is defeated by the actual leviathans. In the long term, however, the leviathans fail. The reapers begin their cycle of accelerating cultural advancement by leaving mass effect technology lying around the galaxy for rising species to find, then absorbing those species once they become advanced enough.
The protheans are the last in a long line of species to fall to the reapers. Though the protheans had learned of the reapers and begun to prepare for their arrival, they were too late. Their preparations survive into the next cycle, however, in the form of the Crucible.
Nuclear conflict devastates the krogan homeworld of Tuchanka, and the advanced society of the krogan devolves into one of warring clans in a post-apocalyptic wasteland.
The asari, the first post-prothean race to encounter the mass effect relays and develop faster-than-light travel, discover Citadel Station.
The Citadel Council is formed after the asari are joined on Citadel Station by salarians, the two species working together to find and unite other civilizations. Contact is made with quarians, volus, hanar, and batarians.
One of the Citadel Council's interplanetary expeditions encounters the rachni after opening a relay leading to systems controlled by their hive mind. The Rachni Wars begin.
The rachni are declared extinct after being defeated by the krogan, who have been genetically uplifted by salarians specifically to combat them. As a reward for their efforts the fast-breeding krogan are given rachni worlds and several planets in Citadel space to settle.
Beelo Gurji, a salarian agent working for the Citadel Council, is accused of using civilians as bait during an espionage operation. Rather than being punished Gurji is promoted, becoming the first Spectre. The Spectres are given greater freedom than other agents and are intended in part to keep an eye on krogan expansion.
The krogan found a colony on the asari world of Lusia. They refuse to depart, so Spectres launch a strike against them. The krogan retaliate, and the Krogan Rebellions begin. First contact is made with turians, who join the war against the krogan.
Turians release the genophage, a bioweapon developed by salarian scientists, which causes a genetic mutation in krogans that reduces the viability of their pregnancies. The effect is devastating.
The long-term effect of declining krogan populations brings an informal end to their threat. Their role at the center of the Citadel military is taken by the turians.
Widespread industrialization on the drell homeworld of Rakhana leads to environmental collapse.
The servants of the reapers called "collectors" are seen in the Terminus Systems, but these reports are dismissed by the Citadel Council as rumors and the existence of the collectors as a myth.
The technologically advanced quarians discover that their robotic servants, the geth, have achieved sentience. Fearing revolt, the quarians begin destroying the geth, which leads to the very revolution they feared.
An asari named Aria T'Loak takes over Omega station and becomes known as the Pirate Queen of Omega.
First contact is made between drell and hanar. The hanar begin evacuating the drell from their dying homeworld, and those drell who survive form a symbiotic relationship with the hanar, which they call the Compact.
Human beings begin to settle Earth's moon, building Armstrong Outpost.
Using information found in prothean ruins on Mars, humans discover that Charon, previously believed to be a moon of Pluto, is actually a mass relay. They travel through it to Arcturus.
Children in Singapore who were accidentally exposed to element zero begin displaying telekinetic abilities. At least, some of them do. Others merely develop cancer.
While activating a mass relay, human explorers are attacked by turians because, to prevent a repeat of the Rachni Wars, the opening of new relays is prohibited. What humans call the First Contact War begins. Turians call it 'the Relay 314 Incident'. You can read more about this in the comic book Mass Effect: Evolution.
Members of the four-eyed batarian species discover the remains of a gigantic, once-living starship called the Leviathan of Dis—a reaper.
Humankind's Systems Alliance becomes an associate member of the Citadel Council.
A member of human-first paramilitary organization Cerberus assassinates Pope Clement XVI using poisoned rosary beads. He is replaced with a pope more agreeable to Cerberus ideals. (Beyond the games, Cerberus are expanded on in the novels, particularly Mass Effect: Ascension and Retribution.)
The Andromeda Initiative, a collaboration between multiple species who plan to send Ark ships to settle the Andromeda galaxy, is founded. Though it will be a one-way trip, their long-term plan is to open a route between the two galaxies.
2183 CE - Start date of Mass Effect
Humans and turians collaborate to create a craft called the SSV Normandy to be captained by the first human Spectre, Commander Shepard. Rogue Spectre Saren Arterius leads an attack on the Citadel on behalf of the reapers and is repulsed. A month later, Mass Effect 2 begins with the destruction of the Normandy and the loss of Shepard.
2185 CE - Main events of Mass Effect 2
Cerberus succeeds in reviving Commander Shepard after two years of effort. The first wave of the Andromeda Initiative departs to settle a new galaxy, having accelerated their plans in response to the reaper threat.
2186 CE - Start date of Mass Effect 3
Reapers invade through batarian space, eventually reaching Earth. Shepard attempts to use the prothean device called the Crucible to defeat them permanently.
In the Heleus cluster of the Andromeda galaxy, first contact occurs between the kett and angarans. The kett appear peaceful at first, but then kidnap angaran leaders and sow discord between angaran worlds.
2819 CE - Start date of Mass Effect: Andromeda
Three of the Andromeda Initiative's Ark ships arrive in the Heleus cluster and are attacked by clouds of dark energy called the Scourge. You can read more about this in the novel Mass Effect: Nexus Uprising.