Hopefully at this point when you return to the CIC EDI will state that she is ready to install the IFF, but that you need to take a shuttle to your next mission because of the downtime on Normandy required to do it. This is mandatory, and you cannot in fact do another mission (a cut-scene triggers when you access the Galaxy Map).
As all of Shepard's squad departs in the shuttle, the IFF goes online, but disables the Normandy's engines and defences, while transmitting its location to the Collectors. A Collector ship arrives on the scene and its inhabitants board the Normandy.
Joker is unwilling to let EDI take control of the ship, so must manually unlock the AI's databases at the AI Core on Deck 3. You take control of Joker for this short section. EDI will show you the way using floor lighting, as the usual corridors are crawling with Collectors.
Once you get control of Joker, turn left and enter the Tech Lab, ignoring the Praetorian that has barged onto the CIC. Enter the Maintenance Shaft in the lab to get onto Deck 3. A crewman offers to cover you through the corridors, so head past the lift to the right while the Collectors are busy with Kelly Chambers.
Use the distraction to limp past the Collectors
Enter the Medical Lab and AI Core and access the controls. EDI needs you to access the primary drive in Engineering next. Once you exit the cut-scene, work up the stairs, stopping to allow the Collectors to move away before turning left into the door behind them. Access the Engineering Controls within. EDI states that she will open the airlocks once the drive is online, blasting the Collectors into space. Joker rightly questions what this would do to the crew, but EDI informs him that the entire crew have been taken. EDI sends a message to Shepard's shuttle.
Once Shepard returns, Miranda lays into Joker for the loss of the crew and nearly the ship. EDI sticks up for him, claiming that she should have spotted the virus. You can choose to berate or comfort Joker for Paragon or Renegade points. At least the IFF is now online, allowing the Normandy to travel through the Omega 4 Relay when you are ready, and begin the final stage of the game. The sooner you go through, the better the chance of saving the crew. If you want to save the likes of Kelly Chambers, you should avoid doing anything else, including the Legion loyalty mission, and just head straight for the Relay. If you do a one assignment, about half the crew survives, but if you take too long, only Doctor Chakwas comes back.
Preparing for the Suicide Mission:
You do have time to mine as many planets as you want before the mission, so make sure you stock up on Element Zero, Iridium, Platinum and Palladium (see Mining walkthrough at the end of this guide). There are three Normandy upgrades that you MUST buy before engaging in the Suicide Mission, as otherwise one of your squad for each missing upgrade will be killed.
The upgrades you need are:
Multicore Shielding, available after talking to Tali: 15000 Palladium
Thanix Cannon, available after talking to Garrus: 15000 Platinum
Heavy Ship Armor, available after talking to Jacob about upgrades: 15,000 Palladium
Upgrade the Normandy before entering the Omega 4 Relay
Spend any resources you have left on weapon, shield and general upgrades for your squad members to give you that extra helping hand on the final mission. In particular, try to max out the Heavy Weapon Ammo (Microfusion Array) upgrades, and personal upgrades, like Mordin's Omni-tool for example. These will have an affect on the final batle.
When you are ready, head for the Omega 4 Relay to begin the Suicide Mission.