'Yan uwan sun yi amfani da fasahar da aka hana ta jujjuyawar mutum don kokarin tayar da ita lokacin da Trisha ta mutu sakamakon annobar. A sakamakon haka, fitarwa ya haifar da rauni kuma a cikin doka tare da musayar daidai, ƙafafun hagu da dukkan jikin Alphonse na Edward sun lalace. Edward ya rasa hannunsa na dama don ceton ran Alphonse, ya ɗaure shi yana da hatimin jini a cikin kayan yaƙi. Roy Mustang ya gayyaci Edward don ya zama hanya don dawo da jikin Alphonse wanda Alan Masana Alchemist na ƙasa zai bincika shi. Edward ya yi nasara, ya zama sunan bisa ga gaɓoɓinsa na ƙafafunsa, mai cikakken Alchemist.
Shekaru uku a gaba, Elrics suna neman Dutsen Masanin Falsafa don cimma burinsu. Marcoh ya aika da bayanansa don su samo su, duk da haka suna koyon mahimmancin abin don yin Dutse shine sadaukarwar mutane. Abokin Mustang, Maes Hughes, yana ci gaba da binciken su, amma an harbe shi da wani kishi da aka ɓoye don gano dabarun Homunculi.
Ganin tare da Izumi, Malaman makarantar sun koyi kwayar halittar mutum wanda ta aikata akan jaririnta. Miyagun halayen gurbatattun kwadayi sun kama Alphonse, amma shugaban Amestris King Bradley ne ya ajiye shi, wanda aka nuna yana aiki kamar fushin homunculus Don haka narkewar kwadayi ya sake zama cikin asalin mahaifi Uban Homunculi. Winry da Elrics sun dawo cikin Babban birni don tafiya tare da Hughes amma sun sami labarin wucewarsa. An tsara Lieutenant Maria Ross don kisan Hughes, amma ana ganin Mustang ne ya kashe shi. Duk da haka, Edward ya san tafiyar Ross an shirya don haka sai Mustang ya shigo da ita daga Amurka zuwa Xing, wanda yariman Xingese Ling Yao ya taimaka. Edward ya sake haɗuwa da Hohenheim amma ya raina shi saboda dogon lokacin da ya yi ba a zaune ba.
Yayinda ci gaban labari yake, Homunculi ya hadu da masu fada aji akai-akai. Mustang yana kashe sha'awa; Mustang da Ling sun kama Gluttony, amma duk da haka ya ƙare cin Hassada a cikin aikin sa, kuma Edward, mai kama da Ling. Gluttony ya ɗauki Alphonse don ya sadu da Uba, amma Ling ya juya zuwa dama, musamman sabon avatar na ƙyashi, lokacin da sauran suka tsere daga cikin Gluttony. An saki Elrics don ci gaba da bin su kasancewar Mahaifin ba ya adawa da su.
Ganin wata ramin karkashin kasa a karkashin Briggs, Janar Olivier Armstrong ya sami Uba kuma Elrics ya kasance yana ƙirƙirar ƙungiyar transmutation ta ƙasa kuma yana da niyyar bawa yan ƙasa saboda ya sami damar hawa zuwa godhood. Kwaɗayi ya dawo yaci amanar Uba da tunanin kansa na baya, haɗuwa da bayan, da Edward, membobin chimera na Kimblee Hohenheim. Hohenheim ya bayyana wa ɗiyansa ɗaiɗaikun cewa shi ba mutum ba ne, ya zama dama ya zama Raunin Masanin Falsafa da Uba ya yi shekaru ɗari huɗu baya.
Ranar wa'adi ta zo kuma Uba ya shirya don fara dabarunsa da kisfewar duhu da kuma waɗanda suka yi ƙoƙari don ɗaukar ɗan adam azaman sadaukarwar sa masu mahimmanci. Manyan jaruman sun yi rikici da membobin Uba, tare da duk Homunculi sun ƙare. Bayan Mustang da aka tilasta, da Elrics, Izumi, Hohenheim an tattara su a matsayin abubuwan da ke haifar da mahaifin kunna fitarwa ta ƙasa. Koyaya, Scar da Hohenheim suna kunna Amestrians don samun ceto ta matakan kariya. Uba ya lalata kwaɗayi, kodayake mahaifin yana fuskantar sama da ƙasa inda jaruman ke yaƙi da shi don su sa dutsen Falsafa.
Alphonse, wanda kayan yakinsa ya lalace amma ta hanyar rikici na ƙarshe da Uba, yana ba da ruhunsa don dawo da hannun dama, wanda shi ma ya lalata Dutse na Uba, tare da mayar da shi zuwa Gateofar Gaskiya ta Edward. Edward ya rasa ikon yin alchemy don dawo da rai da jikin Alphonse. Hohenheim ya ga kabarin inda ya mutu yana da murmushin Trisha.
