Atthebeginningof2259,CaptainJohnSheridanreplacesSinclairasthemilitarygovernorofthestation.HeandthecommandstafflearnthatthedeathofPresidentSantiagowasactuallyanassassinationmastermindedbyVicePresidentClark(whoassumedthePresidencyuponSantiago'sdeath).AconflictdevelopsbetweentheBabylon5commandstaffandthePsiCorps,anincreasinglyautocraticorganizationwhichoverseesandcontrolsthelivesofhumantelepaths.CommanderIvanova,thesecond-in-commandofthestation,issecretlyalatenttelepathwhohasillicitlyavoidedregisteringwiththePsiCorps.                  eee                 　　TheShadows,anancientandextremelypowerfulracewhohaverecentlyemergedfromhibernation,arerevealedtobethecauseofavarietyofmysteriousanddisturbingevents,includingtheattackontheNarnoutpostattheendof2258.CentauriAmbassadorLondoMollariunknowinglyenliststheiraidthroughhisassociationwiththemysteriousMr.MordenintheongoingconflictwiththeNarn.TheelderlyandailingCentauriemperor,longanadvocateofreconciliationwiththeNarn,diessuddenlywhilevisitingBabylon5.Anumberofconspirators,includingLondoMollariandRefa,takecontroloftheCentaurigovernmentbyassassinatingtheiropponentsandplacingthelateemperor'sunstablenephewonthethrone.TheirfirstactistostartopenaggressionagainsttheNarn.Afterafull-scalewarbreaksout,theCentaurieventuallyconquerNarninabrutalattackinvolvingmassdrivers,outlawedweaponsofmassdestruction.Towardstheendoftheyear,theClarkadministrationbeginstoshowincreasinglytotalitariancharacteristics,clampingdownondissentandrestrictingfreedomofspeech.TheVorlonsarerevealedtobethebasisoflegendsaboutangelsonvariousworlds,includingEarth,andaretheancientenemiesoftheShadows.TheyenlisttheaidofSheridanandtheBabylon5commandstaffinthestruggleagainsttheShadows.

ThePsiCorpsandPresidentClark,whosegovernmenthasdiscoveredShadowvesselsburiedinEarth'ssolarsystem,begintoharnessthevessels'advancedtechnology.TheClarkadministrationcontinuestobecomeincreasinglyxenophobicandtotalitarian,andusesamilitaryincidentasanexcusetodeclaremartiallaw.ThistriggersawarofindependenceonMars,whichhadlonghadastrainedpoliticalrelationshipwithEarth.Babylon5alsodeclaresindependencefromEarth,alongwithseveralotheroutlyingEarthAlliancecolonies.Inresponse,theEarthAllianceattemptstoretakeBabylon5byforce,butwiththeaidoftheMinbari,whohavealliedwiththestationagainstthegrowingShadowthreat,theattackisrepelled.                  aaa                 　　BecomingconcernedovertheShadows'growinginfluenceamongsthispeople,CentauriambassadorLondoMollariattemptstosevertieswiththem.Mr.Morden,theShadows'humanrepresentative,trickshimintorestoringthepartnershipbyengineeringthemurderofMollari'smistresswhileputtingtheblameonarivalCentauriHouse.OpenwarfarebreaksoutbetweentheShadowsandtheallianceledbyBabylon5andtheMinbari.ItislearnedthatgeneticmanipulationbytheVorlonsisthesourceofhumantelepathy,asitislaterdiscoveredthatShadowshipsarevulnerabletotelepathicattacks.DispleasedattheVorlons'lackofdirectactionagainsttheShadows,CaptainJohnSheridanbrowbeatsVorlonambassadorKoshNaranekintolaunchinganattackagainsttheirmutualenemy.Kosh'sdeedsleadtohissubsequentassassinationbytheShadows.                                   　　FormerstationcommanderJeffreySinclairreturnstoBabylon5toenlisttheaidofCaptainSheridan,Delenn,IvanovaandMarcusinstealingtheBabylon4spacestationandsendingit1,000yearsbackintimetouseitasabaseofoperationsagainsttheShadowsinthepreviousMinbari-Shadowwar.UndergoingthesametransformationasDelennattheendofSeason1,SinclairtransformsintoaMinbariandissubsequentlyrevealedtobetheactualValenofMinbarilegend,ratherthanareincarnation.Spurredbythereappearanceofhisassumed-deadwife(whonowworksfortheShadows),SheridantravelstoZ'ha'dum,theShadowhomeworld,inanattemptbythemtorecruithim.Howeverheinsteaddestroystheirlargestcityinakamikazenuclearattack,andislastseenjumpingintoamiles-deeppittoescapetheexplosion.Garibaldi,duringafightwithShadowvessels,goesmissing.

In2261,theVorlonsjointheShadowWar,buttheirtacticsbecomeaconcernforthealliancewhentheVorlonsbegindestroyingentireplanetswhichtheydeemtohavebeen"influenced"bytheShadows.Disturbedbythisturnofevents,Babylon5recruitsseveralotherpowerfulandancientraces(theFirstOnes)totheircause,againstboththeShadowsandtheVorlons.CaptainJohnSheridanreturnstothestationafterescapingfromZ'ha'dum,butataprice:barringillnessorinjury,hehasonly20yearslefttolive.HeisaccompaniedbyamysteriousaliennamedLorienwhoclaimstobetheoldestsentientbeinginthegalaxy.                  eee                 　　HoursbeforeSheridan'sreturn,Garibaldiisrescuedandreturnedtothestation,inratherdubiouscircumstances.HeismarkedlymoreparanoidandsuspiciousofotheralienracesandofSheridanthanhewasbefore.                                   　　CentauriEmperorCartagiaforgesarelationshipwiththeShadows.LondoMollariengineerstheassassinationofCartagiaandrepudiateshisagreementwiththeShadows.LondokillsMr.MordenanddestroystheShadowvesselsbasedontheCentaurihomeworld,inanattempttosavehisplanetfromdestructionbytheVorlons.Aidedbytheotherancientraces,andseveralyoungerones,SheridanluresboththeVorlonsandtheShadowsintoanimmensebattle,duringwhichtheVorlonsandShadowsrevealthattheyhavebeenleftasguardiansoftheyoungerraces,butduetophilosophicaldifferences,endedupusingthemaspawnsintheirendlesswarsthroughouttheages.Theyoungerracesrejecttheircontinuedinterference,andtheVorlonsandShadows,alongwiththeremainingFirstOnes,agreetodepartthegalaxyforever.                                   　　AftertheShadowsaredefeatedGaribaldileaveshispostassecuritychiefandworksonhisownasa"providerofinformation".HebeginsworkingforoneWilliamEdgars,aMarsTycoon,whoismarriedtoGaribaldi'sformerlove.WhileheworksevercloserwithEdgars,hebecomesincreasinglyaggressivetowardsSheridanandeventuallyleavesBabylon5.                                   　　MinbarisgrippedbyabriefcivilwarbetweentheWarriorandReligiouscastes.DelennsecretlymeetswithNeroonoftheWarriorcasteandconvinceshimthatneithersidecanbeallowedtowin.Shetellshimthatshewillundergoaritualwhereinshewillbewillingtosacrificeherself,butwillstoptheritualbeforesheactuallydies.WhenNeroonseesthatsheactuallyintendstogothroughtheentireritual,herescuesherandsacrificeshimselfinstead,declaringthat,althoughhewasbornWarrior,inhisheartheisReligious.                                   　　AspartoftheongoingconflictbetweenEarthandBabylon5,GaribaldieventuallybetraysSheridanandarrangeshiscaptureinordertogainEdgars'trustandlearnhisplans.GaribaldilaterlearnsthatEdgarscreatedavirusthatisdangeroustoonlytelepaths.Itisthenrevealed,thatGaribaldiwasactuallyabductedbythePsi-CorpsattheendofSeason3andre-programmedbyBestertoprovideinformationtohimattherighttime.BesterreleasesGaribaldiofhisprogramming,andallowshimtoremembereverythinghehasdonesincebeingkidnapped.Edgarsiskilledandhiswifedisappears,butisreunitedwithGaribaldiaftertheendofthewar.GaribaldihelpsfreeSheridanandreturnhimtothecampaigntofreeEarth.AnallianceledbyBabylon5freesEarthfromtotalitarianrulebyPresidentClarkinashortbutbloodywar.ThisculminatesinClark'ssuicideandtherestorationofdemocraticgovernment.Marsisgrantedfullindependence,andSheridanagreestoresignhiscommission.TheLeagueofNon-AlignedWorldsisdissolvedandreformedintotheInterstellarAlliance,withSheridanelectedasitsfirstPresidentandcontinuinghiscommandoftheRangers,whoaretoactasagalacticequivalentofUnitedNationspeacekeepers.                                   　　Intheseasonfinale,theeventsof100,500,1000,andonemillionyearsintothefutureareshown,depictingBabylon5'slastinginfluencethroughouthistory.Amongsttheeventsshownarethepoliticalaftermathofthe2261civilwar,asubsequentnuclearwaronEarthinvolvinganewtotalitariangovernmentintheyearAD2762,theresultingfallofEarthintoapre-industrialsociety,thelossandrestorationofhumanity'sknowledgeofspacetravel,andthefinalevolutionofmankindintoenergybeingssimilartotheVorlons,afterwhichEarth'ssungoesnova.

　《死亡空间：坍塌》是电脑游戏《死亡空间1》的剧情前传：