ThePsiCorpsandPresidentClark,whosegovernmenthasdiscoveredShadowvesselsburiedinEarth'ssolarsystem,begintoharnessthevessels'advancedtechnologyTheClarkadministrationcontinuestobecomeincreasinglyxenophobicandtotalitarian,andusesamilitaryincidentasanexcusetodeclaremartiallawThistriggersawarofindependenceonMars,whichhadlonghadastrainedpoliticalrelationshipwithEarthBabylon5alsodeclaresindependencefromEarth,alongwithseveralotheroutlyingEarthAlliancecoloniesInresponse,theEarthAllianceattemptstoretakeBabylon5byforce,butwiththeaidoftheMinbari,whohavealliedwiththestationagainstthegrowingShadowthreat,theattackisrepelled
BecomingconcernedovertheShadows'growinginfluenceamongsthispeople,CentauriambassadorLondoMollariattemptstosevertieswiththemMrMorden,theShadows'humanrepresentative,trickshimintorestoringthepartnershipbyengineeringthemurderofMollari'smistresswhileputtingtheblameonarivalCentauriHouseOpenwarfarebreaksoutbetweentheShadowsandtheallianceledbyBabylon5andtheMinbariItislearnedthatgeneticmanipulationbytheVorlonsisthesourceofhumantelepathy,asitislaterdiscoveredthatShadowshipsarevulnerabletotelepathicattacksDispleasedattheVorlons'lackofdirectactionagainsttheShadows,CaptainJohnSheridanbrowbeatsVorlonambassadorKoshNaranekintolaunchinganattackagainsttheirmutualenemyKosh'sdeedsleadtohissubsequentassassinationbytheShadows
FormerstationcommanderJeffreySinclairreturnstoBabylon5toenlisttheaidofCaptainSheridan,Delenn,IvanovaandMarcusinstealingtheBabylon4spacestationandsendingit1,000yearsbackintimetouseitasabaseofoperationsagainsttheShadowsinthepreviousMinbariShadowwarUndergoingthesametransformationasDelennattheendofSeason1,SinclairtransformsintoaMinbariandissubsequentlyrevealedtobetheactualValenofMinbarilegend,ratherthanareincarnationSpurredbythereappearanceofhisassumeddeadwifewhonowworksfortheShadows,SheridantravelstoZ'ha'dum,theShadowhomeworld,inanattemptbythemtorecruithimHoweverheinsteaddestroystheirlargestcityinakamikazenuclearattack,andislastseenjumpingintoamilesdeeppittoescapetheexplosionGaribaldi,duringafightwithShadowvessels,goesmissing
