Virmire

Description
Virmire is a lush frontier world, ideal for colonization by carbon-based species. Its vast seas and orbital position on the inner life zone have created a wide equatorial band of tropical terrain. Unfortunately, the political instability of the nearby Terminus Systems has impeded colonization efforts - the high risk of raids by pirates and slavers makes it an unappealing homestead. The Council's covert salarian STG units ensure that the political instability continues.

Insertion Point and Salarian Camp
Virmire can be accessed after two key worlds have been completed. Commander Shepard is contacted by the Council with a possible lead. They have received a disturbing message sent by a salarian STG unit on Virmire's surface who were investigating Saren's activities. The message contained mainly static, but it was sent through the emergency channel reserved for mission critical communications. Commander Shepard lands on the planet to find there are geth nearby who have set up air assault guns. The team takes out the AA guns so the Normandy can land safely, and continue fighting toward the salarian position in the Mako.

At the camp, Shepard meets Captain Kirrahe, leader of the salarian group, but there's trouble. Kirrahe reports that they've found Saren's base of operations, a heavily guarded research facility. It's a breeding ground for krogan - somehow, Saren has found a way to counteract their genophage. If he can breed krogan at their former rate, he will soon have an unstoppable army and the facility has to be destroyed. Apparently Kirrahe asked for a fleet, but the message was too distorted. The Normandy is all he's getting.

Wrex is furious to hear that Kirrahe is planning to destroy the facility. Saren's discovery might save his species. He storms off down the beach and starts firing his gun into the water. Shepard has to talk to Wrex before the assault; Kirrahe will not go ahead with his plan until Wrex has been dealt with. During the talk Wrex turns his gun on Shepard and may end up being shot (by either Ashley or the commander). If Shepard's Charm or Intimidate skills are high enough, or if the commander has already earned the krogan's trust by helping to recover his family's armour, Wrex finally stands down, agreeing that he doesn't want his people to be Saren's tools and slaves. Now he wants Saren's head in revenge.

Facility Attack
Kirrahe calls Shepard over and explains his plan. The salarians have been able to convert their ship's engine into a small nuclear device that will destroy Saren's base, but the problem is getting it there. The Normandy's presence has alerted the other AA towers on Virmire's surface and they can't drop it from orbit. However, Kirrahe has worked out a strategy. With the Normandy's reinforcements, he is going to divide the forces into four teams. Three of the teams will be salarian, and attack the facility as a distraction to draw the geth out, taking out one of the facility's two AA towers if they can. Meanwhile, a small strike team codenamed 'Shadow', led by Shepard, will sneak around the back and take out the other tower so the Normandy can get in close, carrying the nuke. Shadow Team will set it near the geothermal taps. Once it's armed Joker will pick Shadow Team up - the salarians will escape to a safe distance. But Kirrahe has one more request. He needs a member of Shepard's squad to co-ordinate between the teams. Both Ashley and Kaidan volunteer to go. Shepard has to pick which one to send, then assembles the strike team and gets to work.

Shepard leads Shadow Team down the beach, hearing radio chatter from the salarian attack and fighting off the geth. There are several positions set up by the geth along the way - Shepard can sabotage their communications, destroy their satellite uplink, and destroy their fliers to give Kirrahe's men a better chance. Shepard can also hack into the facility alarms to turn them off. This helps the salarians but means Shadow Team is faced with plenty of guards.

Inside the facility, Shepard discovers captive salarians - members of Kirrahe's recon teams - who have been experimented on and lost their minds, along with an asari scientist named Rana Thanoptis. Rana says that studying Sovereign's indoctrination effect is the true purpose of the facility. Shepard can't work out why Saren would want to study indoctrination if he's the one using it on others. Rana says Saren doesn't fully understand the process - indoctrination is very subtle and Saren is afraid he might be suffering from the effects too. She offers Shepard access to Saren's lab and his private files, but when the team enters the room, they find another Prothean Beacon like the one on Eden Prime. Shepard approaches it and is hit by another vision, but this time the commander remains conscious and is able to cope.

As the squad prepares to leave, a hologram appears of a monstrous creature... Sovereign, which addresses them as "rudimentary creatures of blood and flesh". Shepard realises Sovereign is not a Reaper ship at all, but an actual Reaper. It views Shepard with the contempt it has for all non-synthetics, saying that the Reapers are the ones who created the Mass Relays and the Citadel, to ensure organic life develops according to the wishes of the Reapers. Shepard demands to know what the Reapers want, but Sovereign refuses to answer, saying that Shepard is beneath its notice. Organic life is a genetic mutation, an accident that exists only to serve the Reapers. The hologram disappears, shattering the windows.

Saren's Arrival
Joker radios an urgent message to warn the commander that Sovereign has suddenly changed course and is heading toward them. Shepard continues leading the assault, taking out the facility's AA tower and clearing the ground so the Normandy can bring the nuclear device in. While the nuke is being armed, Shepard gets a call. The salarians - and the squad member Shepard sent with them - are being hit hard at the other AA tower by swarms of geth. They can't hold out much longer. Shepard tells them to sit tight and takes a team to rescue them, but is only halfway to the tower when a geth dropship passes overhead toward the nuke site and starts dropping reinforcements there. As a precaution, the nuclear device is armed - now it will go off no matter what the geth do.

Shepard is then faced with a choice: save Ashley or save Kaidan (one is at the AA tower, the other is arming the nuke). Once the decision has been made Shepard heads to the position, fighting off geth... only to be faced with Saren himself. He appeals to Shepard not to resist the Reapers, because the only way organic life can survive is by being useful to them. Shepard can help him save lives by joining his cause. Shepard refuses, telling Saren he has been indoctrinated and is a traitor to the Council, and they battle. After blowing up a fuel tank Shepard is knocked to the ground, grabbed by Saren, and almost strangled or thrown off the edge of the platform. The commander is saved when the nuke, about to detonate, begins blaring its alarm, distracting the turian and allowing Shepard to break free. Saren gets away - Shepard's team (including the one they came back to save) boards the Normandy, and they escape Virmire just as the nuke destroys the facility and most of the surrounding landscape.

Shepard is then left to deal with the loss of a valued squad member, and console the survivor. Depending on circumstances Captain Kirrahe or Commander Rentola survive with several salarian teammates, and can be found in the Normandy's engineering section. If he survives, Kirrahe offers his condolences and thanks Shepard for the help.