When Shepard uses the galaxy map Joker says the council is amassing a fleet. They want Shepard to submit a report in person. At the Council meeting Shepard finds out they won't do a thing and the Normandy is grounded. After a conversation with a crew member Joker calls saying Captain Anderson wants to meet in Flux. Pick a party. Head to the elevator and ride it down. Use Rapid transit and travel to Flux. Inside Captain Anderson is at a table.
After the conversation, go back to the Normandy. Use Rapid Transit. Choose C-Sec. Enter the elevator. Use it.
Enter the airlock. Use it. Cut scene will show Captain Anderson freeing the Normandy.
Use the galaxy map.
Zoom all the way out. Choose the Pangaea Expanse. Choose the Refuge System. Choose the planet Ilos. A cut scene will begin of the Normandy using the Mu relay. Then another cut scene will start where the crew fights about where to drop. Turn around and follow the path. Shepard will run into some Geth along the way.
Continue on the path and some more Geth will appear, including some Armatures. Continue to follow path south. When Shepard comes to the secure crate, turn right.
Keep following the path. When Sheppard gets to the statue in the patch, go past it. The other path is a dead end.
Follow the path and take a right turn. Follow this path to the courtyard. There will be several Geth in it. Kill them. After the battle go under the upper platform that was to Shepard's left when he entered the courtyard. Follow the path to the back and up the ramp. There will be some Geth Sappers here. Take them out.
After the fight, in the back and a little to the left is an elevator. Enter it. Then use it.
Exit the elevator and turn right. Follow the path. When Shepard enters the room, several Geth will attack, including a Geth Prime. Take them out.
After battle, go north. In middle section will be ramps up to a higher location. Take them up.
Use the Security Panel. A cut scene will begin.
Go back down. Go under the platform Shepard was just on. Follow path to an elevator. Use it.
Shepard will come up where he fought the armatures. Turn and head left. Follow the path back to the Mako and the door Shepard saw Saren enter.
Get in the Mako. Follow the path. Along the way the party will talk about stasis pods on the walls. Shortly after the discussion some Geth troopers will want a fight. Give them one.
Continue on the path until Shepard reaches a force field. Time to bail out of the Mako and disable the field on foot. There is a door on the right side of the path. Enter it. Follow the path. As Shepard enters the elevator, the button to activate it is behind Shepard on the left. Use it.
Exit the elevator. Follow the path. At end will be Vigil. It will talk to Shepard.
Head back to the elevator. Use it. Now go back to the Mako. Get in. Follow the path. The Mako will come to what looks like a dead end, with some Geth troopers at it. Kill them. The path goes to the left. So turn left and follow this path down into the Aqueducts.