The Mass Effect trilogy tells the long and complicated story of Commander Shepard attempting to stop the extinction of all life in the galaxy. Each game serves as its own distinct saga, with plenty of side content to flesh out Mass Effect's vision of the Milky Way and provide character development for Shepard and their crew members. In the first game, the Reaper threat is largely unknown, and focuses on Shepard's investigation into Saren, a rogue Spectre that has betrayed the Citadel Council and now commands a heretical sect of the Geth.
The beginning of Mass Effect's climax takes place on the planet Ilos, when Commander Shepard learns from a Prothean virtual intelligence about the plight of the extinct race and the full extent of the Reaper harvests. Up until this point Shepard has been traveling the galaxy investigating recent Geth activity. Shepard has slowly been able to uncover Saren's motives to facilitate the Reaper invasion, a key part of which appears to be Ilos, a planet that has been unreachable because of a lost Mass Relay.
With evidence of Saren's final goal of reaching a device called the Conduit on Ilos, Shepard informs the Council, who don't believe in the Reaper threat, and are mustering a fleet to defend the Citadel from Saren's Geth forces. With the help of Captain Anderson, Shepard retakes control of the grounded Normandy and uses its advanced stealth technology to pursue Saren through the lost Mu Relay and discover the nature of the Conduit.
Mass Effect 1's Ending: The Reapers' Trap
After the crew of the Normandy follow Saren to Ilos, the ruins of an ancient Prothean research station is discovered. Although the dozens of stasis pods in the facility are deactivated, a Prothean VI called Vigil stands watch over the lab. Vigil reveals to Shepard a greater understanding of the Reapers, and explains the function of the Conduit.
According to Vigil, the Reapers harvest all life in the galaxy every 50,000 years or so. The Protheans, though a highly advanced race, could not figure out why the genocidal machines carry out this cycle. Vigil also informs Shepard that the Protheans' undoing was the Citadel itself, a hidden Mass Relay connected to dark space outside of the Milky Way where the Reapers lie in wait. Built by the Reapers as an attractive location for a major galactic cultural hub, unknown numbers of civilizations have been compromised when the Reapers suddenly appear at the heart of the Mass Relay network.
Though the Prothean race was already doomed, 12 scientists at the laboratory on Ilos came out of stasis in an attempt to thwart future harvests by the Reapers. Ilos had previously been the construction site of a prototype Mass Relay - an effort to reverse engineer the FTL technology. The miniature Relay on Ilos, the Conduit, was a one-way transporter to the Citadel. The Prothean scientists emerged from their stasis pods after centuries, and traveled through the Conduit to alter the signal that alerts the Keepers on the Citadel to activate the dormant Relay within the space station.
With this information, Saren's goal is revealed. While his Geth fleet and the Reaper vanguard Sovereign assault the Citadel from space, Saren will slip onto the station while the defense fleet is distracted to activate the Mass Relay and bring the Reapers from dark space. Shepard then follows Saren through the Conduit, attempting to stop the former Spectre before he can initiate the genocide.
Mass Effect 1's Ending: Pursuing Saren on the Citadel
When Shepard travels through the Conduit, Saren has already had a head start and is moving toward the Council chambers in the Citadel Tower. Shepard and their squad must fight through Geth troops and Mass Effect's feared Krogan warriors bred by Saren. While being pursued, Saren makes it to the Council chambers and takes control of the Citadel, closing the station's massive arms and sealing Sovereign inside. The Reaper latches on to the Citadel and waits for Saren to relinquish control.
Shepard arrives in the Council chambers just in time to engage Saren before he puts Sovereign in control. After besting the ex-Spectre, Shepard uses the control console to reopen the arms of the Citadel, allowing the Alliance fleet to reengage Sovereign. It is here Shepard (and the player) makes a choice that affects the outcome of the final battle. The Commander can either tell the Alliance to focus on destroying Sovereign, or protect the Council, which has taken shelter aboard the advanced Asari starship, Destiny Ascension.
Once the choice is made, Saren's corpse reanimates - a cybernetic husk powered by Reaper technological implants. The final boss battle ensues, and Shepard emerges victorious. Shortly after, Sovereign is destroyed, and debris from the Reaper comes crashing down on the Council chambers, though Commander Shepard is soon revealed to have survived.
Mass Effect 1's Ending: The Fate of the Citadel Council
Depending on the player's choices when opening the arms of the Citadel, there are four outcomes in Mass Effect's final cutscenes dependent on whether or not the Council was saved and Shepard's alignment in the Renegade/Paragon system. If a paragon Shepard orders the Alliance fleet to protect the Destiny Ascension, the Councillors thank Shepard publicly, acknowledging their bravery and loyalty. Renegade Shepard will be thanked behind closed doors, where the Council recognizes Shepard's aggressive servitude toward the existing power structure. Either way, Humanity is granted a seat on the Citadel Council.
If Shepard has a paragon alignment and allows the Council to be destroyed alongside the Destiny Ascension, a new Citadel Council is formed among the Citadel races with a Human chairman. Non-Human species are left out of a new Council if the Destiny Ascension is not protected by a renegade Shepard, and Humanity comes out of the final battle as the most powerful and influential race in Citadel space.
No matter who winds up comprising the governing body, the Councillors turn their focus to the delayed but looming Reaper threat. The most immediate concern, which Commander Shepard is recruited for, is hunting down the remaining Geth Heretics who aligned themselves with Sovereign. For their role in uncovering the Reaper threat and confronting Saren, Shepard becomes widely recognized as the savior of galactic civilization. Shepard's actions at the end of Mass Effect draw the attention of the Illusive Man, the enigmatic founder of the anthropocentric terrorist organization Cerberus, which plays a major role in Mass Effect 2. The Illusive Man believes Shepard's talents are being wasted by the Alliance hunting down rogue Geth factions instead of finding a more permanent solution to the Reapers.