May contain spoilers!
We last left off with the choice of what character you were going to leave with Captain Kirrahe. I really did not use Kaiden very often, so I felt that he was the character I could leave behind. After this point you can start making your way into the back way of the facility.
The first group of enemies you will run into will be protecting the Communication Tower. As long as you keep cover and use your sniper riffle you should be able to easily handle the majority of the Geth. If you are looking for Paragon points you can shut down communications which would help Captain Kirrahe.
Continue to make your way past the enemies. There are monitor objectives that can be completed on your way into the facility. Once you reach the facility you can disable the alarms. With this you are given the option to send the enemies to the front of the facility. If you don't think you can handle them yourself you can choose that option. I however decided to fight them myself.
Most of the difficult stuff is out of the way. Make your way through the facility and shut down the AA guns so you can get set the nuke. While going through the facility you will come across some of the prisoners that Saren has been experimenting on. You can free them to gain Paragon points, or leave them or even kill them.
When looking to shut down the AA weapons you will come into contact with an Asari named Rana Thanoptis. She has been working for Saren and offers to get you into his private chambers. You notice that there is another Beacon here. As you activate it you see some of the same images from the first beacon.
When the cut scene is complete you notice and have a long conversation with Sovereign, a Reaper. They are real after all. How are you going to convince the counsel of this? You will worry about that later. You have to shut down the AA weapons so that you can set the nuke.
Taking the elevator down to the Breeding Grounds you will encounter a few more Geth. After finishing them off you are finally able to shut down the AA weapons. With the AA weapons down the Normandy can bring in the nuke. You tell Kaiden to meet you at the rendezvous point. He is pinned down with the crew he is with. Once again you will have to make a choice, Ashley or Kaiden.
If losing one of your team members was not enough the timing of Saren showing up definitely does not make things better. Saren believes the only way to save himself and others is to work with the reapers. This is why he has been doing the things he has. The worst part about it is that he believes he is doing the right thing. After the conversation ends there is a battle between your crew and Saren. Do what ever you can to attack him, but make sure to find cover. After the battle you will enter the end mission cut scene...
Next up: Return to the Citadel.