The game starts of with the two boys [ Edward and Alphonse Elric] performing a Human Transmutation to revive their dead mother which results in failure and skips ahead to their mission involving the false prophet Cornello to find the fabled Philosopher's Stone to amend for the things they lost in the failed Human Transmution [Alphonse's body and Edward's limbs]. They suceed in proving him as a swindler but find the Philosopher's Stone to be fake. The brothers head back to Central to report it when the train gets hijacked by Bald 's group which threatens with a hostage. The Elric brothers rescue the hostage who reveals herself as Corniche Royce and find that the boss was merely an imitation of Bald. The Elrics learn that the girl possesses ability to use healing alchemy and is heading towards Central for State Alchemy Exam . Corniche decides to tag along Elrics as she hasn't traveled before. The train gets attacked by a Chimera and stops at a town named Viva. The trio rescues the town which is swarming with Chimeras but fail to find the culprit. They continue their journey towards the Central. After reaching central Corniche goes to the Military Headquaters for her exam but realizes that she has forgotten her essay. While she is insisting on her participation, King Bradley appears and sets up a condition for her certification- to beat Major Alex Louis Armstrong. Corniche fails and Edward is summoned by King Bradley for Chimera's extermination in East City mission. Edward is also given a permission to form a 'Special Squad'. After much insistence from Al and Hughes Edward agrees to recruit Major Armstrong and Colonel Roy Mustang in the special squad though he despises the idea of working with the two. The party takes Major Armstrong from the Central and heads towards the East City where Colonel is assigned and mission to be executed, but on their way the train gets hi-jacked again by real Bald's group who threaten with the life of all passengers. The party defeats the culprits and reach the East City and travel directly towards the Colonels office. Colonel Mustang refuses to join and leaves for a surveil which makes Edward more determined to recruit him. The party chases Mustang and challenges him with a fight to decide his enlistment. After being defeated Colonel is forced to join and Lieutenant Riza Hawkeye volunteers to help for Colonel's safety. State Alchemist Lieutenant Colonel Aston Martins also known as The Thunder Alchemist is enlisted upon Mustang's insistence. Mustang leaves his paperwork on East City Chimera's case to Havoc and heads towards Redendo along with the rest of the party. The party solves the robbery case at Redendo but comes empty handed with their true assignment. Back at the East Military Headquaters Party learns about a case of two people described as one short and one in armor causing disturbance at a town named Solin. Hoping that it would lead to some kind of clue to Chimera case and dubious of perpetuators identity party travels to Solin. There the party learns that the people causing trouble indeed look like Elric Brothers and infact call themselves Elrics too. Infuriated with their name being disgraced again by imposters, the Elrics decide to catch the charlatans. Once they capture and defeat the imposters, the party learns that are merely alchemist created manikins again and the alchemist is no other than a young girl aged 16 who reveals her name to be Cate Rham. Cate makes a brief encounter with the party and then flees saying that they'll again someday. With the fakes revealed and still clueless about the Chimera's case the party returns to the East Headquarters again. Once back at the East Headquarters the party learns about an eccentric alcehmist living in a mansion who is assumed to possess skills in body alchemy. Suspicious, the party head towards hermit's mansion and learns that the strange man is indeed involved in Chimera's case, but before they can arrest him, they are attacked by a Chimera and the suspect flees. Colonel contacts the HQ and learns that the man is named Dalt Daimler and he's heading towards Edward and Alphonse hometown Resembool . The party fails to find Dalt in Resembool but Ed gets his maintenance. The party head towards ruins near Resembool where Dalt is likely to be. While chasing Dalt the party meets up with two of the Homunculi: Lust and Gluttony whom they defeat. After defeating the Homunculi Edward mentions his suspicion to Alphonse about Philosophers Stone presence in ruins as the homunculus were around. However, the brothers agree to keep this theory a secret. The party finds Dalt corpse which is missing a bag that Dalt was carrying. The party moves on to find out the murderer who turns out to be Randy the robber at Redondo. The party defeats Randy and starts to interrogate him about the surrounding situation before Cate intervenes along with a masked alchemist named Lincor whom Colonel Martin seems to know as Licor takes Dalt's bag from Randy and uses a tremendous power to unleashe a powerful attack on the party and earn enough time to escape with his group. Ed conjectures that Licor was using a Philosopher's stone in Dalt's bag to wield such power. Meanwhile, Mustang and Martin discuss that how strangely Linor's presence resembles that of State Alchemist Colonel Seraphy Royce. Mustang tells Ed about Seraphy Royce's history who was a healing State Alchemist [The Tuning Alchemist] whose qualification was about to be taken from him before he was reported dead in Ishval War. The trio suspects if he was the one responsible for recent Chimera's outbreak and if Corniche Royce is really Lincor's sister. The party receives information about Licors hideout in East City Sewers and goes there. Though it's unable to find Lincor, the party encounters Lincor's associates Cate and Randy again and a a man with a scar on his forehead who vaguely claims to pass down the god 's judgement . Colonel Martin is reluctant to fight his 'old friend' so he suggests the party to retreat as they are unlikely to find Lincor. As the party is heading towrds HQ, when it learns about Chimeras assault on HQ from Hughes. The party exterminates Chimera's from the base mainly to safe Mustang's address book in his office. While still in Mustang's office, the party further discuuses Lincor's case where Corniche learns about her possible relevence to Lincor. Ed encourages her to believe in her brother which Corniche accepts to do. After the party rescues the HQ, Mustang gets caught up in restoration paperwork with Riza by his side. Other miliraty members also get engaged leaving Ed, Al, Corniche and Colonel Martin (as their bodyguard) to have a break. The group decides to spend the night at Inn. At that night Martin asks Edward his reason for being the Dog of the Military. Edward explains about his failed human transmutation and his determination to restore his younger brother's body back. Corniche tells the brothers that she believes they'll suceed in achieving their goals and then the group has a dinner. The next day, the group decides to head back to HQ as there might be new info on Lincor's case. The whole party assembles again and head out to a castle in southeast where Lincor's sightings have been reported. The party meets Lust, Randy,and Cate again all of whom they defeat again separately. On there way to meet Lincor Mustang mentions his suspicion on Martin who openly refuses the charge. The party finally catches up with Lincor. Ed provkes Lincor to reveal the Philosopher Stone in the bag but Lincor opens the bag and unleashes a giant ultimate Chimera instead. The Chimera keeps regenerating .With no other option at sight, Martin sacrifices his own life to defend his party. With a dear friend sacrificed, Ed gets agitated and questions Lincors motives to hurt his very own friend and sister to which Lincor answers by saying that something valuable is a necessary price to protect something and Martin was fool not to understand that. Ed attacks Lincor who drops a locket which holds his and Corniche's photo. Corniche questions Lincor if he really is her brother who would hold the words 'Alchemist, Be Thou for the People' dear but Linor bluntly refuses of having any recollection of her and violently attacks the party. The party defeats Lincor but he refuses to give up. Ed sums up all the events and concludes that the power Lincor possess is not by using the Philosopher's Stone but by trading his precious memories with his sister. Licor makes one last attempt to annihilate the party by merging himself with the whole castle. Corniche remembering Martins words to stay strong to be State Alchemist heals the whole party which emerges victorious again. Lincor recalls his remaining memories of his mother and feeling that he traded everything for peoples' welfare dies comfortably. The party once again heads back to HQ. Back at HQ, the party recovers from their former friend's death and Corniche is finally allowed to retake State Alchemy Exam. Corniche passes the exam and earns her brother's title 'The Tuning Alchemist'. She gladly accepts it and decides that she would recompense for her brother's wrongdoings. The story comes to an end with Corniche separating from the Elric brothers for her hometown and everyone else settling back their normal lives.