For those interested this is a guide to what EGM has changed. The document contains extensive spoilers.

Do not read this if you want to experience the mod fresh.

NORMANDY

Entire Ship

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Marines - numbers can be set in the manifest.  Need to have appointed a Marine Lieutenant.
A well built Marine Sargeant will wander the ship if there are enough Marines on the Normandy.
Normandy Stereo (plays throughout ship). Button on each deck.
Reaper War notifications - Alliance Intel reports on the war, hints to locations of GAW Assets.  Customised to playthrough.

Ship's Manifest - allows the player to customise the Normandy. Some crew members must be spoken to before they can be appointed.
Crew manifest reflects in game history (e.g. Tali exile/admiral, Garrus trained as Spectre or C-SEC, Vega N7 etc.)

Crew: Appoint XO (gives XO's datapad to the crew member selected, receive mails from the XO about visitors)
Crew: Appoint LT (must have military background, gives LT's datapad to the crew member selected)
Crew: Appoint Chief Engineer (Tali or Adams only)
Extra crew adjustments: Marine security level, medics, engineers, facilities.
Medics, engineers and facility technicians give small bonuses. All others do not unless stated.

Normandy - configure cargo deck layout, vehicles, mechs etc.
Change non-crew squadmates

Revised Terminal:
Spectre Mail replaces training videos.
Squad menu allows changing appearance and also squadmates powers
Ships Manifest - Squad, Crew, Equipment
Normandy mail shows rank, surname, name

DECK 1
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Cabin invites - love interests can be invited up once locked in.  They will hang about the cabin and a variety of cutscenes will play. Jack available post Grissom only if ME2 romance and flirted with at Grissom.
Romance chocolates if purchased for the LI will appear in the cabin.
What food/drinks are shown depend on the on-board chef
Other items depend on different characters

Medal Case - showing game achievements
Cabin picture - showing love interest once locked in.
Fornax - once purchased or found.
Corporal Campbell's Mug - if claimed during the Citadel DLC.
3 extra models above bed - ground vehicles
Prothean Sphere - found in mission if had in ME2 or can be purchased.
N7 Helmet - (if imported from ME2)
Fish can be fed by either feeder, chef or manually.
Kai Leng's Broken Sword
If installed and completed: Miranda Mod - Cerberus Cruiser Model; Ark Mod - Turian Fighter Model
Entire terminal can be accessed from either the CIC or Cabin

Fixed - desk glow
Fixed - armor locker will unload the cabin to reduce memory usage (with aggressive memory management)

DECK 2
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Bridge
EDI's Holo is restored between Priority: Mars and Priority: Palaven (with ambient conversation).
Cockpit shutters
Cockpit entry door used if at Citadel (optional)
Fixed - sticky patches on bridge floor
Fixed - Garrus floating post tuchanka scene

CIC
Revised Personal Terminal with Spectre Mail, Squad screen allows powers to be changed, Crew Manifest and Normandy Manifest.
CIC access to war room data via second terminal
Flashing notifications of war room data, new emails, new spectre mails
New war asset - Prothean translator - once Traynor tells you that Javik has given the program

War Room/Conference Room
Bodyguards - for  leaders on the Normandy - including Primarch, Wrex/Wreav, Dalatrass and Quarian Admirals.

Fixed - war asset emitter now switches off properly.

DECK 3
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Visitors:
Jack and Grissom Students (post Grissom Academy, Jack must be loyal)
Grunt in Medbay (must survive Rachni mission)

Extra Crew:
Medical Staff - select up to 2 staff, must appoint a Chief Medical Officer first, and read mail. Each gives a small combat bonus.
Facilities Specialist - select a Chef or Barman.  Must appoint a XO first.  Both will feed your fish.
Chef - food will be available in the mess hall.  If the security level is high a marine will hang around chatting up a girl crew member.
Barman - drinks will be available in the mess hall.  A marine might be found drinking at the bar.

Battery
If Garrus is dead and after Priority: Palaven is complete a crewman will take the post of Gunnery Officer.

Medical
Cybernetics terminal available once Prothean implants are found and mail from Glyph is read.
Squadmate power reset - includes Javik and all new squadmates.
If extra medics are appointed occasionally a crew member will be in sickbay.

Liara's Office
New screens:  SB screensaver, planet view, chlorine planet, Crucible plans, Thessia (post invasion)
Normandy SR1 photo (if romanced in ME1)
Illos picture from apartment (if LOTSB is completed)
Short hugging scene on bed if Liara is romanced (or if loyal romance rekindled in LOTSB and confirmed during first convo)

Fixed: Shadow Brokers screens fixed in place so they don't wobble or invert.
Fixed: FTL effect seen on both windows, not just one.

Starboard Observation Lounge
Ashley - when she drinks herself stupid, a datapad will appear with background info on what happened to her team.  Follow up data is on the Shadow broker terminal. All give clues to a GAW asset.
Kaidan - once you have heard him chat to EDI about his students, a couple of missions later a datapad will appear with info on them.   Follow up data is on the Shadow Broker terminal, with clues for a GAW asset.
Books - Ascension and Revelations codex (if you had in ME2)
Books - Haiku from Kasumi can be read (if she joins the war effort)
Window shutters

Fixed: FTL effect

War Memorial
Another former crew member will appear if you find out information on his fate.
Fixed: Zaeed will appear if he died in ME2 or ME3.

Port Observation Lounge
Window shutters
Liara conversation after the Coup is available if you didn't kill Ashley / Kaidan. (Requires EXTRA add-on - English only)

Fixed: FTL effect
Fixed: Glasses that don't line up on the shelf

Crew's Quarters
Occasionally Corporal Campbell will leave a webbrowser open so you can access Morlan's Pawn Shop. This contains odds and ends from across the Galaxy.
Removed window covering so Engine Room can be viewed as per ME2.

Life Support
Weapons will appear in the racks if security setting is high or Thane is aboard (with TM3)
Working desk - pads and computer added
Training screens can be accessed (if Thane is not on board)
Removed window covering so Engine Room can be viewed as per ME2.

Fixed: graphical glitch on Thane's mug

DECK 4
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Extra Crew:
2 of 6 possible Engineers can be added after Rannoch is completed (need to read email from Tali or Adams). One engineer requires the Quarians to survive and ME2 assignment Omega: Struggling Quarian. Each engineer gives various bonuses, depending on what technology is installed on the ship.
Normandy upgrades terminal - shows which upgrades are installed (including ME2 imports), allows purchase of further upgrades. Upgrades to the ship impact Galaxy Map performance.
Shooting Range, Mechbay add the items to Deck 5. 
Medical upgrades (ME2) adds equipment to the medbay on Deck 3.
Removed window covering in port and starboard cargo holds so you can observe the main cargo deck.

DECK 5
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Visitors:
N7 soldiers - post pickup N7 Extractions assignment
Geth Primes - once recovered during Geth Fighter Squadrons
Aralakh Company - once recovered during Rachni mission (includes ambient conversation)
Shadow Broker Wet Team - includes the giant salarian Tazzik from the comics - once recovered.
Geth Fighter (with Tali, Ran and Xen) - once used to escape from a Geth Dreadnought.
Legion preparing the Geth equipment - before Geth Fighter Squadrons.

Extra Crew:
Marine Platoon - post Rannoch, if Marine setting is highest.
Marine engineer - if marine level is medium or higher, and a ground vehicle is carried.

Optional equipment:
Shooting Range - with crew comments on how you are doing, 4 different target sets, choice of using armored or casual. A small bonus is available if you practice enough.
Mechbay - up to 2 mechs can be carried.  They can be purchased or found during the galaxy.  5 different to collect.
Vehicles - the secondary vehicle is destroyed by Vega on Mars.  You can salvage or purchase other vehicles to replace it. 13 different vehicles available.
Javelin missile battery - cost depends on choices during ME2's  Javelins Launched mission. Purchases adds upgrade to Normandy GAW.  Requires ME2 mission (or fresh ME3 install).
Anti personnel guns - requires Marine setting to highest.
Armory - shows weapons collected (vanilla, CE, Leviathan, Omega, Citadel DLC)
Hydraulic decking - raise the deck near the secondary vehicle.
ME2 Weapons import case.  If you import weapons from ME2 (not new game plus). Will be cleared away after 7-8 missions.
Fornax - interaction with James (requires magazine purchased in ME2)
Mechdog - can be purchased from Alliance Requisitions, added conversation options.
Normandy Requisitions - Alliance requisitions available with extra armors and other usually only available late in the game.
Windows unlocked - can see the port/starboard cargo holds

Fixed: Armor locker memory management (optional)
Fixed:  Cargo deck name appears on back wall
Fixed:  Floating objects on Cortez desk
Fixed:  Graphical glitch underneath the shuttle area
Fixed: Removed window covering in port and starboard cargo holds so you can see into those rooms. Also fixed stars visible through crack in deck 4 ceiling.


GALAXY MAP

Over 50 restored systems, entire galaxy map is unlocked from the start.
Planets will change descriptions as they are invaded.
Fuel depots in most systems that will disappear and become destroyed once invaded.
Reapers will only appear in invaded systems, and can be switched off in most situations via EGM Settings.
Specialist Traynor will make occasional comments if a system has assets in it.
Relay video can be customised via settings.
Icons show major fleet locations (optional)

Notes on war assets:
- All vanilla and many new war assets are available. Nothing has been removed, but a few have been moved (largely where Bioware made lore errors).
- Generally war assets are only available once the system has been invaded - it doesn’t make sense that they need rescuing before.
- Some assets, where it makes sense, are available before invasion e.g. an ancient artefact that can be used by the crucible, and they are still available after invasion as well.
- The war reports contain hints, and stories behind the assets.
- On each cluster there is a % that refers to the cluster's available assets that have been recovered.  Unfortunately blank can either mean nothing available or nothing found (an ME3 issue).

Generally it is best to do a search of newly invaded systems not at 100% after each mission. Once invaded all the assets are usually unlocked. But it is, of course, up to the player.


Notes per cluster:

ME3 Changed
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Widow
- Bekenstein restored, Alliance 5th Fleet depot, Refugee fleets, fuel depot restored to widow.
Ismar Frontier
- Aquila, Elysta restored.  Zoyra Industrial support available if Blue Suns have been recruited and the plant was saved in ME2.
 - Salarian Research station is available as part of the Ismar Frontier Components mission.   It replaces the intel being found on a random gas giant.
Exodus Cluster
- Prothean Data files GAW are now on Terranova, not a gas giant.  Terranova planet skin has been fixed.  Asteroid X57 appears if BTDS is completed in ME1.
- the Allied Fleets gather here before attacking Earth.   The fleets are customised to the players playthrough.
Sigurd's Cradle
- the Javelin Missile launchers is available on Franklin if the factories are saved during ME2's Javelin mission.   If not volunteers from Watson City can be found.
Olyn Protectorate
- this was partly finished and hidden in the ME3 map files, and restored in conjunction with the Thanemod team.
Petra Nebula
- Elysium gets invaded earlier (approx 7-8 missions in) so Grissom Academy has to be done before that point.
Argos Rho
- Pinnacle Station's GAW is only available if the Vidinos is beaten during the ME1 DLC.   The station will be destroyed when the Reapers invade.
Far Rim
- Near Charom where the Geth fleet is stationed, there is a debris field reflecting the Quarian attack.
Hourglass Nebula
- Shadow Broker ship and base are now reverted to their lore friendly locations.


ME2 Restored
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Phoenix Massing - Sea of Storms - Heretic station appearance and GAW depends on outcome of ME2 A House Divided.
Omega Nebula - Omega 4 relay, Omega
Hawking Eta - (ME1/2)  If the biotic cult led by Major Kyle are not killed in ME1, they can be recruited.
Pylos Nebula - Kriseroi, Saherin (ME2), The Geth Weather device can be used as a crucible component if ME2 N7: Anomalous Weather Detected assignment was completed.
Eagle Nebula
Rosetta Nebula
- the Dealer is here (near the planet Jacob's father crashes in ME2).  
- Iota Urania - a system that was in ME2 but never seen has been unlocked.
Local Cluster - Gagarin station has been added.  Pluto re-skinned.
Titan Nebula - A GAW is available if all the ME2 mech missions were completed.
Caleston Rift - Solveig, Talawa, Yakawa.  The radiation shield is available as a Crucible component on Solveig if the ME2 mission N7: Endangered Research Station was completed.
Minos Wasteland - Caestus
Crescent Nebula - Tasale
Far Rim - Ma-at.
Tartarus - orbit the Omega 4 relay to access.  Cut scene plays.


ME1 Restored
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Horsehead Nebula - Fortuna, Strenuus (GAW available once you rid the Nebula of Cerberus and if you defeated some Privateers in ME1)
Voyager Cluster
Panagea Expanse - Ilos (note Refuge has 2 suns, reflecting the ME1 vision rather than the ME1 map)
Sentry Omega - Virmire (note a short video memorial to the person who died in ME1 will play)
Armstrong Nebula - GAW here dependent on ME1 mission Geth Incursions
Artemis Tau
Styx Theta
Maroon Sea - note GAW are available depending on ME1 missions Colony of the Dead, Exogeni Scientists and Turian Insignias


ARMOR & WEAPONS

All armors (including vanilla) are available with separate torso and helmets or as a full body outfit. You have to set the arms/legs/shoulders to none, otherwise you will get clipping with full body torso armors.

Unless stated otherwise they can all be purchased at Alliance Reqs or via the Dealer.
* indicates unique power setup
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Parts Armor (HR & Tintable)
Spectre Armor (found on Citadel after a new human spectre is appointed)
MOHLE Backpack*
Breather Mask
X4 Rangefinder (headgear found in game)
Stratos Helmet (Dealer only)

N7 Armors (all HR & Tintable)*
T5-V Battlesuit
Broshep only - N7 Slayer, N7 Paladin
Femshep only - N7 Fury, N7 Demolisher, N7 Shadow
Note one armor will be given free by the Alliance after completing the N7 assignment. Which depends on the gender and class of Shepard.

Alliance Armors
Marine (Broshep)
Marine officer (HR Tintable)
Alliance Special Forces (Heavy & Medium) [Tintable]

Mercenary/Other Armors
Operative* (Ashley variant Fem, Vega variant Bro)
Corsair*
Battlefield (Broshep)
Garmr Heavy Assault (CAT-06, Spectre Reqs or Dealer)*

Retro Armors
Colossus (found on Normandy as a gift for Anderson)
Phoenix (Femshep)
Duelist Armor (Harrotts or Volus store)
Mercenary Armor (Harrott's only)

Cerberus Shock Trooper armor can be found in a Cerberus mission.
Collector armor can be salvaged.
Terminus armor can be found in a colony. (with Ark Mod)
Blood Dragon Armor can be found in a house on Eden Prime.

Weapons
Collector Assault Rifle, Collector SMG, Collector Sniper (all salvaged)
Spectre M-57 Gladius (found after a new spectre is appointed)
Pistol Ultralight V (needs Leviathan DLC.  Weaker versions must be purchased first, not new game plus).


ASSIGNMENTS

These are enhanced fetch quests - just like the existing ones to find things in the galaxy map, apart from a small choice or difference test to complete them.  Some give Paragon/Renegade points, some give war assets, others credits. They are just different and hopefully more interesting ways to do these types of quests.

15 Assignments:
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Assignment: N7 Extractions (must be done prior to Priority: Tuchanka)
Assignment: Bekenstein (must be done prior to Priority: Tuchanka)
Assignment: Aria's Forces (must be completed prior to Omega DLC)
Assignment: Criminals vs Veterans (will happen a few missions after meeting Aria and if Garrus is aboard.  You have only 1 mission to complete, will only fire if Omega DLC is not yet complete)
Assignment: Phoenix Project (Requires Cerberus Labs to be complete)
Assignment: The Strontium Mule
Assignment: Find the Rachni (Requires Rachni queen to survive)
Assignment: Batarian Attack
Assignment: Aite
Assignment: Collector Cruiser (Requires From Ashes DLC, Leviathan DLC)
Assignment: MinuteMan Station
Assignment: Evacuation of Thessia
Assignment: Geth Supplies (requires Geth to survive, ME1 Geth Incursions mission to be completed)
Assignment: Prothean Sites


The Dealer - unique store enables the player to exchange discovered artifacts for high end armor, weapons and other tech.  The Dealer will be introduced by the Shadow Broker a couple of missions after Palaven.

Existing Fetch quests - these have been changed so you need to unlock the quest in the Citadel first.  This includes Elcor Extractions.  Dekuuna Code of the Ancients can only be recovered during the Evacuation of Dekuuna.


SQUADMATES

Squadmates have a variety of outfits to wear during off duty moments on the Citadel and Normandy. Some require DLC, Squadmate Pack or Custom Extras.
Tali has extra armor (hood down).

Additional Squadmates - Wrex, Jack, Miranda, Jacob, Samara, Grunt, Kasumi, Zaeed and Aria.
6 N7 missions unlocked for them by default, 8 additional missions can be unlocked via a special pack.
Default (Citadel DLC) armors plus alternatives for Jack, Grunt, Samara, Jacob, Kasumi and Zaeed.
Which squadmates who are available for missions can be set via the Crew manifest.


GALAXY AT WAR

Alliance Intel Service - 20 reports on battles and events during the war, customised to your playthrough.
EMS - the final GAW EMS (final score) is now set before you go to Earth, rather than before Cerberus HQ.

Revised Galaxy at War system:
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Reorganised system:
- Fixed various lore errors
- New categorisations to remove Aliens catch all
- N7 troops reflect lore from multiplayer of troops coming together as special forces.
- Battles, events and losses now reflected
- Crucible upgrades impact the Crucible, not engineers.
- Minor irregular units combined into single units.

Major decisions have greater impact:
Salarians always contribute something, however will contribute considerably more if the genophage is sabotaged. Salarians commit fully if their Councillor is dead and the Council died in ME1 - it forces them to assume the other races will not win without them.
Asari support will be greater if Shepard saved the Council in ME1, as the Asari media idolise them.
Krogan will be the strongest ground army by far
Alliance has all the fleets from lore, and a mechanised division
Geth are impacted more than the Quarians from the decision on Heretic station
Geth fleet is now heavily damaged by the Quarian Alarei tech as per lore

Many assets now relate back to ME1/2 decisions including: Major Kyle, Javelin missiles, Overlord & many more.


INTEL & CYBERNETICS
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Weapons Training - Bonus intel can be acquired by practicing on the range. Once the player has used the range a few times and broken a number of shields, a bonus intel that give a a choice of either a small bonus to weapon damage or a bigger bonus to headshot damage.

Prothean Cybernetics - after Surkesh a message will appear in the Spectre terminal requesting help when some researchers are attacked whilst investigating Prothean ruins. Go to the destination and you can recover powerful cybernetics. Once you read an email from Glyph telling you that the intel is available, you can head to the medbay to use it. The intel has both positive and negative bonuses. Further schematics can be found at different Prothean locations in the galaxy, only 1 per main mission. All possible locations are highlighted on the Galaxy Map.

Cybernetics
- All users - Weapon Heat Dispersion - +100% shot capacity prior to reload.
- All users - Health -30% or -20% if one of the schematics is applied.

Schematics - available as you discover new Prothean sites.
- Cunning - Sharpshooter specialist - Headshots +150%, Weapon Damage -20%
- Agility - Speed specialist - Speed +30%, Shields -30%, Shield Regen +20% faster
- Leadership - Generalist - Ammo +30%, Grenades +1, +30 GAW Upgrade to Alliance Marines, -15% Health
- Rage - Melee specialist - Melee Damage +250%, Speed +15%, Health +15%, Shield Regen 35% faster, Weapon Damage -25%
- Vengeance - Power specialist - Power Damage +120%, Power Cooldowns doubled
- Fury - Blitz specialist - Power Cooldowns 195% faster (time about halved), Power Damage -30%
- Strength - Tank specialist - Shields +225%, Shield Regen time almost doubled (for Vanguards power cooldown a third slower)

The cybernetics and schematics can be changed and swapped out whenever you want, with a short cooldown period to allow surgery to heal.

GENERAL IMPROVEMENTS

Gameplay - during combat missions:
H - toggle helmet on/off
P - port arms - lower the weapon from raised

Citadel - elevator is available to all players no matter their DLC configuration - direct access back to the Normandy.
70+ Codex items from ME1/2 (and some cut ones from ME3) restored to fire at relevant time.
Mission bonus - if your crew survived ME2 and you had a Prothean Sphere, you can find out what happened to it during an N7 mission.
Grunt email - email from Grunt is now available in all situations where Grunt lives, not just to those who kill the Rachni.
Priority: Mars Loadout - select armors and weapons when in the prologue mission to Mars.

ACHIEVEMENTS

12 new achievements to collect including the ultimate completionist for doing every single mission, side mission, collectable throughout the entire series in a single playthrough.

For more information read the Achievement guide.

EASTER EGGS
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There are numerous small easter eggs - however there are 3 bigger ones on the Normandy Cargo Deck.
(1) Dependant on a ME2 squadmate being loyal, who is visiting and whether your Normandy is a noisy place.
(2) Dependant on your whole trilogy play-through and which vehicle you are carrying.
(3) Dependant on a ME2 squadmate surviving, the setup of the cargo deck equipment and buying something from an odd store.

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