Stop the Collectors

Cerberus has determined that an alien race called the Collectors is attacking human colonies. They are assembling a team to stop this threat to humanity.

Acquisition
This mission is acquired automatically after the completion of Freedom's Progress.

The Stop the Collectors mission is the main plot mission in Mass Effect 2, which mainly consists in answering requests from the Illusive Man that will lead Commander Shepard's team (which will build-up along the way) throughout the Terminus Systems, in an effort to deal, by any possible means, with the uncovered Collectors threat.

Walkthrough
The Stop the Collectors mission starts right after Shepard has found evidence that the Collectors are the force behind all of the recent abductions of entire human colonies in the Terminus Systems. It only ends when Shepard attempts to deal with their base on the other side of the Omega 4 Relay, whatever the outcome.

Assemble a team (1)
After returning from a field investigation at Freedom's Progress with Miranda and Jacob; Shepard has a meeting with the Illusive Man. During the meeting Shepard learns that the team's findings of evidence incriminating the Collectors as responsible for the mass abductions of human colonies confirms the Illusive Man's pre-existing suspicions. Then Shepard, despite any possible misgivings about working with Cerberus, agrees that Cerberus's effort to oppose this new threat upon the Galaxy appears genuine and is worthy of Shepard's involvement. The Illusive Man then tells Shepard that he should start by assembling a strong team for their now common effort. He explains that most of Shepard's former team has scattered throughout the galaxy and is either unavailable, unaccounted for or difficult to convince to work with Cerberus. The Illusive Man then presents Shepard with a list of possible recruits to consider, based upon Cerberus's intelligence (Dossier: Archangel, Dossier: The Convict, Dossier: The Professor, Dossier: The Warlord and, if you have registered the DLC "Cerberus Network", Dossier: The Veteran and Dossier: The Master Thief). Shepard and the Illusive Man also discuss the question of involving the Galactic Council, which is left to Shepard's judgment. The Illusive Man then specifies that Miranda and Jacob will continue to serve under Shepard's command. When ending the meeting the Illusive Man pleasantly surprises Shepard by providing an initial crew member whom Shepard already knows very well; Joker. Joker then leads Shepard to a second large surprise, their ship; the new Normandy SR-2. This part of the mission ends when you have recruited what is considered a sufficient core team (by completing the first four Dossier missions).

Go to Horizon
This new part starts right after you first task is considered sufficiently completed (will not trigger until you have recruited Jack, Garrus, Grunt, and Mordin). Once triggered, you cannot do any other mission (cannot access the galaxy map). An urgent message from the Illusive Man explains that Cerberus has received a warning of a possible new Collector attack on the Horizon human colony. He requests that you go there immediately, to attempt to stop the attack, but also, and more importantly, to gain a better understanding of the attacks and to research a way to oppose new ones.

Assemble a team (2)
This part of the main mission requires you to recruit additional squad members, and the following dossiers are added: Dossier: The Assassin, Dossier: Tali and Dossier: The Justicar. This part of the mission ends when you have completed five assignments, dossier, or loyalty missions.

Investigate Collector Ship
The Collector Ship mission triggers after you have recruited 8 team members and have done 5 missions since Horizon (5 mission completion screens). Once triggered, you cannot do any other mission (cannot access the Galaxy map). If you don't wake up Grunt, he doesn't count as a team member.

You are sent to investigate a disabled Collector ship in order to determine how to use the Omega 4 Relay without being destroyed.

You leave after EDI hacks into the mainframe of the ship and discovers they use a Reaper IFF to get past the Omega 4 Relay.

Acquire Reaper IFF
You travel to a dead Reaper to get its IFF transponder. When you arrive you discover that it is not dead but mostly disabled, and as you fight your way to the core and the IFF you get help from an unexpected source.

You obtain the IFF, kill the Reaper, and have the option to recruit a new member to your party.

Await IFF Installation
After you have acquired the IFF, Commander Shepard has to wait until the installation has been completed.

The time limit for Reaper IFF installation is unpredictable. In some cases, where all previous missions have been completed prior to the IFF mission, the IFF can be activated immediately after the IFF mission. (In this situation, it is important to activate Legion prior to accessing the Galaxy Map. Otherwise, it is impossible to perform Legion's loyalty mission and also save the Normandy crew.) In other cases, the player is allowed many more missions to be completed before the IFF is installed. More confirmation is needed.

Once the IFF is installed, EDI will inform the Commander that the IFF is almost ready. Accessing the Galaxy Map will trigger an irreversible event where the Collectors will ambush the Normandy and abduct the entire crew minus Joker.

Once the IFF is installed you have a choice, either head to the Omega 4 Relay, or continue completing assignments. If you choose to go immediately, you will save the entire crew. If you do 1 to 3 assignments, then you will lose half the crew, including Kelly Chambers. If you do 4 or more assignments, then you will lose the entire crew except for Doctor Chakwas.

Use Omega 4 Relay
This is the point of no return. Before you use the Omega 4 Relay, make sure that every team member is loyal and the Normandy's fully upgraded with shielding, armor and the Thanix cannon. If your ship is not fully upgraded or some of your team members are not loyal, parts of the crew might die during the Suicide Mission.

Defeat the Collectors
You have used the relay and crash landed on the Collector base's hull, now you have to go in and destroy it. This mission varies by who is in your party and if you gained their loyalty by doing their side missions. At the end of the mission you finally find out why the Collectors were abducting humans.

You kill the Collectors and either Shepard or Joker talks with the Illusive Man one last time, this conversation varies based on your final decision (the sequel's version of conversation after the Battle of the Citadel).