Mass Effect lore launched humanity into the future with the discovery of the Prothean ruins on Mars in 2148. With access to a malfunctioning mass effect core and numerous starships, the people of Earth were able to advance their technology and travel beyond the Sol system for the first time. Time and interaction with the Citadel Council races revealed that the mysteriously extinct Prothean race was well-known all throughout the galaxy, but no one had a clue about what happened to them.
As Commander Shepard began the Reaper threat, they discovered on Ilos that the Protheans' disappearance was brought on by a Reaper invasion, and in time, the Reapers repurposed Prothean DNA to create the Collectors. A highly advanced race, the Protheans fought to evade extinction, and though they failed, they were close to developing something that could destroy the Reapers once and for all. Dr. Liara T'Soni has been studying the archives, and after Reapers hit Earth with a devastating attack, Admiral Hackett sent Shepard to Mars to rendezvous with Liara and learn about the mysterious Prothean weapon.
Mission: Find Liara
Before advancing toward the facility, take a moment to level up Shepard, James Vega and Kaidan/Ashley. Shepard receives a new weapon here based on their class. Adepts and Engineers receive the M-4 Shuriken. Soldiers, Vanguards and Sentinels get the M-23 Katana. Infiltrators gets the M-92 Mantis. With everyone leveled up, equipped and ready to go, start moving toward the base. After jumping down through the gap in the fence, pick up the M-92 Mantis on the ground, examine the body for XP.
You'll quickly discern that the soldiers below are Cerberus Assault Troopers, and they are executing civilians. Because of Shepard's position here, they can be taken out easily from higher ground. Advance through the attempted Cerberus ambush, taking them out before reaching the compound and entering the elevator. Inside the elevator, a cutscene occurs where Shepard can speak with their former squadmate (Kaidan or Ashley depending on who survived Virmire) about Shepard's loyalty to the Alliance or Cerberus. Shepard's responses here can net Morality points, with Paragon replies helping rebuild the squadmate's trust in Shepard and Renegade responses fostering their mistrust.
As the lift arrives, the party discovers Liara in combat with Cerberus. As she takes them out, she explains that she discovered plans for a Prothean device that could wipe out the Reapers. Now, they need to get to the Archives to get the plans. Shepard sends Vega back to the Normandy, and Liara joins the squad for the remainder of the mission.
Mission: Get to the Archives
After the cutscene ends, combat launches again. Take out the Cerberus troopers, then pick up the med-kit before attempting to access the elevator. The elevator has been sabotaged, so use the lift to the reach the upper ramp and jump across. Turn right and open the door, where the game issues a prompt on how to grab and kill and enemy from behind. This launches another round of combat, so finish off all the troopers and head into the next room. Check the datapad on the chair and then enter the control room. Examine the locker to pick up the Ariake Technologies Gauntlets, then advance a little to find the M-4 Shuriken and another med-kit.
Unlock the doors and head outside and down the ladder. Pick up the Kassa Fabrication Chestplate at the end of the walkway and climb the next ladder. Head into the maintenance tunnel leading into the darkened cafeteria to investigate the dead bodies. Go down the stairs and toward the controls in the next room.
There will be Cerberus troopers on the other side of the shutters, so take cover and listen to their dialogue. Shepard can use the grab-kill maneuver here to take out one of them, and then take out the others. Pick up the SMG Scope from the Cafeteria, then hop over the wall to access the medical station. Upon reaching the environmental controls, watch the footage to discover that the new doctor, Dr. Eva, was the one who opened the airlock and killed everyone.
Advance through the doors and pick up the SMG Ultralight Materials before accessing the datapad for XP. There is a weapon bench at the bottom of the stairs where Shepard can change the loadout and add any upgrades they have to Liara's weapons. Once finished here, go up the stairs and battle through the next wave of Cerberus agents, which now includes Centurions and Guardians, as well as Troopers. Grab the datapad from the right hand corridor then head left. Cerberus is retreating as Shepard advances, and upon entering the hatchways, they can be heard calling out, "Fall back to the tram station."
Access the control panel that sterilizes the next room and move all the barriers around so they are open. Once all are open, activate controls, enter the room and pick up the med-kit, Sniper Rifle Extended Barrell and Shotgun High Caliber Barrell. Head out the door on the far right, then turn right to find the M-23 Katana (if Shepard does not already have it). There is a ceiling turret here, and Shepard will need to take cover and move when it's safe to the next cover point. Open the door on the other side of the room and take out the Cerberus agents. There is a med-kit and datapad, as well as a Sniper Rifle Concentration Mod in this room. Upon using the auto-turret controls, Shepard discovers that Cerberus has implanted Reaper tech into their soldiers.
Board the tram and activate the controls. An explosion causes the car to get stuck, and a Cerberus cable car rushes toward it. Take out the soldiers, then hop across to that car and activate it. Prepare for an ambush upon reaching the station. There are two waves of enemies in this fight, the second containing Cerberus Guardians. After the fight, grab the M-15 Vindicator, the Shotgun Shredder Mod and scan the medical station for XP. Use the nearby weapons bench to change loadout if necessary, then advance into the archives.
Mission: The Prothean Archives Chase
Inside the Prothean archives, a holo of the Illusive Man engages Shepard. This conversation can net morality points, but it's ultimately a distraction so Dr. Eva can get what she came for. Kaidan/Ashley discovers her, starting a chase through the archives. It's imperative to stay close to her, not stopping for anything, as getting more than 40 meters away from her will cause the mission to fail. Attacking her is all but useless, as it doesn't really slow her down much and she regenerates her shields instantly. Battling through Cerberus is what makes this tough, as there is very little time to stop and shoot soldiers in the way.
Chase her to the shuttle. Just as she's about to escape, Vega crashes his shuttle into hers. Dr. Eva emerges from the fiery crash, exposing her true nature as an AI while her organic disguise melts and burns away. She picks up Kaidan/Ashley by the face plate, and as Shepard begins heading toward her to stop her, she begins slamming them into the burning shuttle. Once she drops them, she runs at Shepard in slow motion, at which point Shepard must fire at her with as many pistol rounds as they have to take her down. Shepard orders Dr. Eva's body be taken in for study, then runs to their wounded squadmate.
This mission makes it clear that Cerberus and the Illusive Man will be as much a threat to Shepard and the rest of the Galaxy as the Reapers, but there's not much time to consider that at the moment. With the mission complete and the data retrieved, Shepard must head straight to the Citadel to get Kaidan/Ashley the medical attention they require and to speak with the Council about aiding Earth against the Reaper threat.