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