ThePsiCorpsandPresidentClark，whosegovernmenthasdiscoveredShadowvesselsburiedinEarth'ssolarsystem，begintoharnessthevessels'advancedtechnology.TheClarkadministrationcontinuestobecomeincreasinglyxenophobicandtotalitarian，andusesamilitaryincidentasanexcusetodeclaremartiallaw.ThistriggersawarofindependenceonMars，whichhadlonghadastrainedpoliticalrelationshipwithEarth.Babylon5alsodeclaresindependencefromEarth，alongwithseveralotheroutlyingEarthAlliancecolonies.Inresponse，theEarthAllianceattemptstoretakeBabylon5byforce，butwiththeaidoftheMinbari，whohavealliedwiththestationagainstthegrowingShadowthreat，theattackisrepelled.BecomingconcernedovertheShadows'growinginfluenceamongsthispeople，CentauriambassadorLondoMollariattemptstosevertieswiththem.Mr.Morden，theShadows'humanrepresentative，trickshimintorestoringthepartnershipbyengineeringthemurderofMollari'smistresswhileputtingtheblameonarivalCentauriHouse。 Mexiko kwazakagawakuwotcherweentheShadowsandtheallianceledbyBabylon5andtheMinbari.Iislearnedthatgenet icmanipulationbytheVorlonsisthesourceofhumantelepathy，asitislaterdiscoveredthatShadowshipsarevulnerabletotelepathicattacks.DispleasedattheVorlons'lackofdirectactionagainsttheShadows，CaptainJohnSheridanbrowbeatsVorlonambassadorKoshNaranekintolaunchinganattackagainsttheirmutualenemy.Kosh'sdeedsleadtohissubsequentassassinationbytheShadows.FormerstationcommanderJeffreySinclairreturnstoBabylon5toenlisttheaidofCaptainSheridan，Delenn，IvanovaandMarcusinstealingtheBabylon4spacestationandsendingit1,000yearsbackintimetouseitasabaseofoperationsagainsttheShadowsinthepreviousMinbari-Shadowwar.UndergoingthesametransformationasDelennattheendofSeason1，SinclairtransformsintoaMinbariandissubsequentlyrevealedtobetheactualValenofMinbarilegend，ratherthanareincarnation.Spurredbythereappearanceofhisassumed-deadwife（whonowworksfortheShadows），SheridantravelstoZ'ha'dum，theShadowhomeworld，inanattemptbyt h emt但是，它卻破壞了測試的可能性，在城市中測試了米卡澤尼核攻擊並最終跳向了阿米爾-深坑逃脫了爆炸。