Reaper IFF

To pass through the Omega 4 relay safely, the Normandy will need a Reaper designed "Identify Friend/Foe" (IFF) device. One of these Reaper IFFs may be found on a derelict Reaper hulk being investigated by Cerberus.

Acquisition
Upon completion of the Collector Ship mission, the Illusive Man will give Shepard the location of a derelict Reaper in order to acquire its IFF. A Cerberus team is currently investigating it. The Reaper is orbiting the brown dwarf Mnemosyne in the Thorne system in the Hawking Eta cluster. Depending on how many of the Normandy's crew that the player wants to survive the game, the player may want to wait commencing this mission until all recruitment and loyalty missions, except for Legion's, are completed.

Preparation
You will be facing hordes of Husks in this mission, with a sprinkling of Scions and Abominations. In other words, you are primarily dealing with armored opponents who come straight at you, and should prepare accordingly. Because of the rate that the Husks will be coming at you, some additional priorities should be considered:
 * 1) On higher difficulties it is paramount to have an area effect ability that can strip armor: Mordin with Incineration Blast, Zaeed with Inferno Grenade, Samara with Area Reave.
 * 2) Once armor is stripped from a group of husks (or on lower difficulties where they are unarmored) they can be instantly finished with physics-based attacks. Once again area effect abilities is where it's at. So Jack with Shockwave, or any of the biotics with Throw Field, or any of the soldiers with Concussive Blast. Note that Pull Field is slightly less effective because the husks die only after the duration has expired, rather than instantly. The Adept's Singularity will usefully tie up groups of husks and make them easy targets, and will produce some insta-kills.
 * 3) On all difficulties it is useful to bring a character with an ammo power effective against armor, especially when evolved to be shared with the whole squad. So Garrus with Armor-Piercing Ammo, Jack with Warp Ammo, or Jacob/Grunt with Incendiary Ammo.
 * 4) Grunt is perhaps the most "no-brainer" squad member choice, because in addition to Squad Incendiary Ammo for armor stripping and Concussive Blast for physics-based insta-kills, his melee charge attack can kill multiple husks in one attack, regardless of armor. Finally his health regeneration and barrier abilities make him almost impossible for the husks to take down - a high level Grunt can literally run through husks for the whole mission and never go down even on Insanity.
 * 5) If husks are frozen with Cryo Ammo and Cryo Blast, they will shatter automatically (no followup shot or ability required). This only works when their armor has been stripped, of course.
 * 6) On lower difficulties Sentinels can "suicide bomb" with Tech Armor, which will kill all husks in the radius. Does not work on husks with armor.

Cerberus Ship
Go through the door. On the left, there is a small laboratory with a wall safe that can be bypassed for 2,000 credits, a terminal accessible for another 2,000 credits, another wall safe bypassed for 4,000 credits, and a work log. Dr. Chandana is the leader of the Cerberus research team. His log indicates the beginning of Reaper indoctrination of his team. At the end of the hallway are two medical stations, and a work log by a Cerberus scientist, reporting on the examination of specimens inside the Reaper. Dr. Chandana was apparently "listening" to the specimens.

Go through the airlock into the Reaper itself. The Reaper activates its kinetic barriers. Joker radios that the Normandy cannot retrieve them until the barriers come down. EDI advises destroying the mass effect core to remove the barriers. However, the mass effect core also powers the mass effect fields that prevent the Reaper from falling into the brown dwarf.

Reaper Interior
Across the catwalk the next work log plays the message:

As soon as you pass by an explosive crate, Husks and an Abomination appear. It is best to backpedal and to blow up the crates when Husks are nearby. Husks only have melee attacks, so it is wise to keep your distance. Also, Abominations do suicide charges and will explode upon death, no matter how they died. Throughout this level in certain areas, Husks spawn by climbing up over the sides of the walkways. There will also be numerous explosive items mainly explosive crates and containers. Use them wisely, because the husks can quickly overwhelm you and your squad. Using Overload on an explosive item produces a larger blast than just shooting it. Try to only use Overload on an explosive item when there is a mass of enemies nearby to maximize the effect.

Once the Husks are down, move up to the next set of crates and be prepared for another fight. There will be more here so the nearby explosive crate is useful. Just make sure that your squadmates are not using the crates for cover. After that group is sent to oblivion, your party comments that this proves that husks must be made from Reaper technology, not geth. There's another work log in this area that plays the message:

Head down the walkway to see and hear gunfire from an unknown party shooting Husks. Your party makes the comments about another person being on the ship. At the end of the walkway are power cells, 2000 units of platinum, a sniper rifle damage upgrade, and a terminal with 3,500 credits. Turn left into an open area. Take note of the cover, explosive items, and locations of thermal clips before moving too far in. Once you move in waves of Husks and Abominations attack. A Scion is in the final wave. You can retreat back to the walkway if you need a breather or more thermal clips.

If you are very fast in bypassing and willing to forego the Heavy Skin Weave upgrade, you can go to the right after the first wave, bypass the door, leave the area, and skip the fight. However, any attack on Shepard will interrupt the bypass and you have to start the bypass over. Note that following the bypass there is a brief (several seconds) "airlock procedure" during which you will need to stay alive. Fortunately as long as you take down the first wave of husks before attempting this, the huge hordes that spawn for the last wave won't make it into this passage in time to stop you.

Once you defeat all the enemies, walk to the other end of the room. At the end of the area are a med kit, and a hackable terminal which will give the Heavy Skin Weave upgrade. Some Dragon's teeth are visible, and if Jacob, Garrus, or Tali are present, the person will comment upon them. You can earn some morality points based on your dialogue choice. A work log catercorner from the hackable terminal will play the message:

"Chandana said the ship was dead. We trusted him. He was right. But even a dead god can dream. A god — a real god — is a verb. Not some old man with magic powers. It's a force. It warps reality just by being there. It doesn't have to want to. It doesn't have to think about it. It just does. That's what Chandana didn't get. Not until it was too late. The god's mind is gone but it still dreams. He knows now. He's tuned in on our dreams. If I close my eyes I can feel him. I can feel every one of us."

Once done here, head to the airlock and on to the next area.

Reaper Exterior
Bypass the door and go through the airlock. A cutscene starts. A geth sniper with bits of N7 armor attached to it snipes several Husks by Shepard's party. The geth says, "Shepard-Commander," then leaves. More Husks and an Abomination soon appear; deal with them and then put your squad into cover and walk down the stairs. Once you go past the crate in the center, there will be Husks, an Abomination, and a Scion. You can retreat back upwards to make the stairs as a chokepoint. Since Husks are melee enemies, it is generally best to stay "on the move" rather than getting in cover - this makes it much less likely you will be trapped by husks, and by moving around you will often confuse them. Obviously as the Scion approaches you will need to either interpose objects between you and it, or move perpendicular to the line of its shockwave. The site of the first battle after you leave the airlock makes a good battlefield-of-last-resort to pull back to - you have room to run around to dodge husks but also the giant tank on the right side to interpose between you and the Scion.

Once the enemies are dealt with, go up the stairs at the other end. To the left will be Medi-gel and a terminal with 3,000 credits. Advance carefully because moving too far will result in attacks by more Husks and one Abomination. Once they are down, nearby there is a terminal with 3,500 credits. Down the stairs are more Husks, Abominations, and a Scion. Use the stairs as a choke point again and then take them out. Once done, a Medi-gel, a shotgun damage upgrade, and power cells await you at the bottom of the stairs. Further on, up the ramp, are a bunch of thermal clips and a terminal with 3,500 credits. This area will be crucial in the next fight.

The next battle will be Husks, Abominations, and two Scions. This battle will be tough no matter the difficulty because of the amount of enemies that come at you. The Husks will charge at you. Keep your squadmates, and yourself for that matter, back or you will regret it. Use powers, specialized ammunition, and shotguns for close up damage when you need to. One way to finish this area easily is to retreat back to the room you just came from, where only three or so husks and the two Scions will approach, since the additional husks only spawn when you get close again. Once the Husks are down, focus on the Scions. The Scions will approach last and are easier to deal with than the Husks; the best thing is to take one yourself and use your squadmates against the other. Once they are down, move on but be careful. Once you reach a left turn, get ready because Husks, Abominations, and two more Scions will come crawling over the railings and from the core. Take them out and do not be afraid to backpedal if necessary.

After they all have fallen, pick up the power cells and a little further down, grab the Medi-gel. Bypass the door and enter yet another airlock. Inside is the Reaper IFF and a wall safe that can be bypassed for 2,500 credits.

Mass Effect Core
Once you enter, the game auto-saves and a cutscene plays. The geth sniper from before is manipulating some controls. It drops a barrier allowing Shepard and the team inside. However, Husks overcome the geth and knock it out.

The objective of the battle is to destroy the Reaper Core, but an iris often closes to cover it, preventing any damage. The iris is open at the beginning, but closes when attacked or when the initial Husks are dead. It will stay closed for between 45 seconds and a minute. Subsequent closures are between 30 and 45 seconds in length. Meanwhile, waves of Husks and Abominations attack you. They respawn as long as the Core is closed, but they always come from the same areas every time. Use that to your advantage if you start to get overwhelmed.

You can only damage the Core when it is open. It will stay open until you have taken its health down by a third, so do not feel pressured into immediately firing into it when it opens up - just take pot shots whenever you're presently safe from husks. When the Core is open, enemies do not spawn, so it is possible to eliminate them all, then sweep up thermal clips and let powers recharge before shooting up the Core, though this may of course result in the spawning of more total enemies. Squadmates will also revive when the Core is open and all enemies are dead, so it may be best to put off using Medi-gel if the Core is going to open soon. The thermal clips around the room will regenerate so there is no lack of ammunition as long as you can get to them. Unlike the rest of the level, there are no handy explosive items. On the lefthand side, there's a laptop with 1,000 credits. It must be taken during battle since there will be no opportunity to walk around the area afterwards.

Every enemy here is effectively a melee opponent, so mobility is key. If you can just avoid being trapped/surrounded by husks you can keep on the move and be fine. Your best position, when possible, is the top of the central bridge from which you have a commanding view of both sides of the room and can throw area effect powers at the masses of husks. But if things get too hot on the bridge then flee down to one side or the other where there is more space to dodge around - remember the husks aren't very good at stopping and turning around, and use their lack of maneuverability against them. Strip armor from groups of husks (e.g. with Incineration Blast), then annihilate them with physics attacks (e.g. Throw Field, Concussive Blast, etc).

The Core is not a "targetable" object, so be wary if you are using the Missile Launcher to damage it. It will tend to lock onto other enemies instead of going after the Core, unless you are at the apex of the center walkway. The M-920 Cain can destroy the Core in one shot on any difficulty. The easiest method to getting through this area is to not move when the battle begins (as the Core will remain open while you're far away and the Husks are still alive), switch to the Cain, and shoot the Core. This will end the battle immediately.

Normandy
Once the battle is over, a cutscene plays. The party debate what to do with the fallen geth, but Shepard makes the decision to take it with them. Joker brings the Normandy alongside the falling Reaper. The squad retreats while pursued by hordes of Husks. They take advantage of the microgravity and toss the geth into the Normandy's airlock and jump in afterwards. In the debriefing, Miranda states that the geth is being stored in EDI's AI Core. Jacob and Miranda debate what to do with the recovered geth. Jacob is in favor of tossing it out the airlock. Miranda wishes to give it to Cerberus. If you decide to the talk to the geth, it will stay onboard deactivated, waiting for you to talk to it, and you gain 20 Paragon points. You can also hand the geth over to Cerberus for 50,000 credits and 20 Renegade points, but Legion is permanently lost as a potential party member.

E-Mail Messages
For completing this mission, and deciding to keep Legion, Commander Shepard receives this message from the Illusive Man.

Alternatively, Shepard receives the following e-mail, in case Legion is handed down to Cerberus:

Mass Effect 3 Consequences
If Legion was sold to Cerberus, it will appear as an enemy during Priority: Cerberus Headquarters, and a Geth VI will take its place during the three missions it appears in. If it wasn't activated at all, the same will happen. If it was activated, assuming it survived the suicide mission, it appears in the aforementioned missions and it will be possible to gain both geth and quarian allegiance.

Enemies

 * Abomination
 * Husk
 * Scion

Mission Summary
Reaper IFF successfully retrieved. Loss of Cerberus team on the Reaper vessel unfortunate but unsurprising. Will use team's health records for comparisons against husks encountered on Reaper for possible insight into indoctrination and husk conversion process.
 * Experience reward: 1,000 (1,250)
 * Credits: 50,000
 * Cerberus Funding: 25,000
 * Credits Found: 25,000
 * Upgrades:
 * Heavy Skin Weave (Lattice Shunting)
 * Sniper Rifle Damage (Scram Pulsar)
 * Shotgun Damage (Synchronized Pulsar)
 * Minerals:
 * Platinum: 2,000

Trivia

 * It is possible to see Legion standing at far end of the room when you turn left after the two husks are dropped by its sniper fire. If you look around in the back of the room the shots came from and zoom your weapon, Legion can be seen standing on the ledge at the back. It will walk away once you enter the room.