Virmire is a lush world located in the Terminus system. It has a multitude of features that appeal to organic life, including oceans, Jungles and very favorable temperatures. However, it is in the lawless Terminus system and due to the inherent risks of piracy and raids it has not been colonized yet. Saren Arterius sets up his secret medical facility here where Krogans are cloned.
Once the player gets to Virmire and enters orbit, Joker informs you that there are a lot of anti-aircraft turrets and that you will have to take the MAKO and that you will have to shut the turrets down. You are dropped in a little river of sorts and in addition to some local wildlife, which are completely harmless to you the place is overrun with Geth. The Geth are there in force and include armor units like the monstrous Colossus. After fighting through the multitude of enemies you reach the first barrier of sorts, which has controls to the anti-aircraft barricade. After you disengage another turret the Normandy is free to land. You are also informed that there is a Salarian encampment a few clicks from your position and you proceed there. As you reach the encampment, you are greeted by an Salarian named Captain Kirrahe and he informs you that he is part of the STG (Special Tasks Group) and that he was here to take stalk of the situation. He looks shocked to see that you have only brought a small crew and he tells you that he requested that the Citadel sent a fleet. He goes on to tell you that Virmire houses Saren’s main medical base and that they are developing a cure for the genophage. He also tells you that the Base must be destroyed so that the “mistake” of unleashing the Krogan is not committed again.
If you agreed to take aboard Wrex on the Citadel, he makes an appearance and he warningly tells you that the Krogan are not a mistake before angrily storming away. Captain Kirrahe looks extremely perturbed by Wrex and asks you if you can deal with him and make sure things don’t get out of hand. You tell him that you will do so and you go to confront Wrex, who is busy trying to shoot down Birds. Immediately upon entering into the Conversation, Wrex accuses you of not giving back to him and points out that he has stuck behind Shepard in every instance. If your charm/intimidate skills are high enough you can convince him to stand down. If you use the charm action you can point out gently that the cloned Krogan are not really a part of his Race as they work for Saren who is using them as cannon fodder, alternatively if you chose to use Intimidate you can drive home that point more forcefully.
However, if your Charm/intimidate skills are not high enough you will be forced to put down Wrex.
You can do this in a few ways, you can signal Ashley to shoot him from afar, you can shoot him yourself, otherwise when the conversation starts going south, Ashley will automatically kill him saying better him that you. Regardless, once you have “dealt” with Wrex, you go and talk to Captain Kirrahe who gives an inspiring speech to his men and tells you about his plan to attack the facility. His plan involves you splitting into two squads, with his main force directly attacking the facility, which will almost certainly entail in death. He says that you and your smaller squad will use the diversion to sneak around the relatively unprotected back and will destroy the facility. He asks you for one of your squad mates, either Kaiden Alenko or Ashley Williams to be part of his team. He reasons that this would help better facilitate communication in between the squads. Along the way he advices you to look for opportunities to undermine the Geth operations in the area, such as knocking down communication towers and such. After you decide on either Kaiden or Ashley, you proceed with the mission. It is immediately clear that Captains Kirrahe’s distraction has succeeded as you face a very small contingent of enemy forces.
You will enter the facility through the far entrance and you will have to work your way to the middle-front of the facility to reach the main lab section. Eventually after wading through Geth and Krogan alike you will reach a holding area which will contain mindless Salarians, the same Salarians who were part of Captain Kirrahe's commandos group. In fact, if you talk to him before you start the mission he will tell you that he sent out scouts who did not return. After you kill them, you will have the choice of taking a elevator up to the labs or proceeding through another door.
There you will encounter another Salarian who seems hell-bent on getting out of his holding facility. He tells you that he hears an incessant noise coming though the cell wall. If you have Wrex or Ashley in the party they will advice you not to let him out. Either way he will freak out and end up knocking himself out by running into the cell door. After, you have dealt with the Salarian you can take the elevator up to the labs and you are promptly encountered by a multitude of Krogan and Geth. The lab area is large and you will have to work your way through the facility. Of note is the fact that the organics in the facility are really immersed in their work; on one such occasion a Krogan will come running to face you shouting about how the work he is doing benefits his race and that he will not let you destroy it. They almost seem a little mad. After you succeed in destroying everything in the facility, you proceed through a door to further reaches of the facility. Also, Captain Kirrahe and the rest of the main squad advices you that they are under heavy attack and have taken casualties.