| No. | Original | Japanese | Romaji | Meaning |
| 1,2 | Emissary | 聖なる神殿の謎 | Seinaru Shinden no Nazo | Mystery of Sacred Temple |
| 3 | A Man Alone | 宇宙ステーション殺人事件 | Uchu Station Satsujin-jiken | Space Station Murder Case |
| 4 | Past Prologue | スペース・テロリスト ターナ・ロス | Space Terrorist Tahna Los | Space Terrorist Tahna Los |
| 5 | Babel | 恐怖のウイルス | Kyoufu no Virus | Terrible Virus |
| 6 | Captive Pursuit | ワーム・ホールから来たエイリアン | Wormhole kara Kita Alien | Alien Come from Wormhole |
| 7 | Q-Less | 超生命体“Q” | Cho-Seimeitai Q | Ultra-lifeform Q |
| 8 | Dax | 共生結合体生物“トリル族” | Kyousei-ketsugoutai-seibutsu Trill-zoku | Symbiotic Combination Creature Trill |
| 9 | The Passenger | 宇宙囚人バンティカ | Uchu-shujin Vantika | Space Prisoner Vantika |
| 10 | Move Along Home | 死のゲーム | Shi no Game | Deadly Game |
| 11 | The Nagus | 宇宙商人フェレンギ星人 | Uchu-shounin Ferengi-seijin | Space Merchant Ferengi |
| 12 | Vortex | エイリアン殺人事件 | Alien Satsujin-jiken | Alien Murder Case |
| 13 | Battle Lines | 戦慄のガンマ宇宙域 | Senritsu no Gamma Uchu-iki | Trembling Gamma Quadrant |
| 14 | The Storyteller | 混迷の惑星“ベイジョー” | Konmei no Wakusei Bajor | Confusing Planet Bajor |
| 15 | Progress | 第五の月“ジェラドー” | Dai-go no Tsuki Jerrado | Fifth Moon Jerrado |
| 16 | If Wishes Were Horses | 夢幻の刻 | Mugen no Toki | Fairy Time |
| 17 | The Forsaken | 機械じかけの命 | Kikai-jikake no Inochi | Mechanical Life |
| 18 | Dramatis Personae | 反逆のテレパス・エネルギー | Hangyaku no Telepath Energy | Traitorous Telepath Energy |
| 19 | Duet | 謎のカーデシア星人 | Nazo no Cardassia-seijin | Mysterious Cardassian |
| 20 | In the Hands of the Prophets | 預言者の導き | Yogensha no Michibiki | Prophet's Lead |
| No. | Original | Japanese | Romaji | Meaning |
| 47 | The Search, Part I | ドミニオンの野望(前編) | Dominion no Yabou | Ambition of Dominion |
| 48 | The Search, Part II | ドミニオンの野望(後編) | Dominion no Yabou | Ambition of Dominion |
| 49 | The House of Quark | クワークの結婚 | Quark no Kekkon | Quark's Marriage |
| 50 | Equilibrium | 仮面の幻影 | Kamen no Gen'ei | Illusion of Mask |
| 51 | Second Skin | 恐るべき過去 | Osorubeki Kako | Terrifying Past |
| 52 | The Abandoned | 捨て子の秘密 | Sutego no Himitsu | Secret of Abandoned Child |
| 53 | Civil Defense | 暴徒制圧モード始動 | Bouto Seiatsu Mode Shidou | Rioter Repress Mode Starts |
| 54 | Meridian | 次元移動惑星M | Jigen-Idou Wakusei M | Dimension Moving Planet M |
| 55 | Defiant | 奪われたディファイアント | Ubawareta Defiant | Bereft Defiant |
| 56 | Fascination | 恋の感謝祭 | Koi no Kanshasai | Thanksgiving of Love |
| 57 | Past Tense, Part I | 2024年暴動の夜(前編) | 2024nen Boudou no Yoru | Year 2024 Night of Riot |
| 58 | Past Tense, Part II | 2024年暴動の夜(後編) | 2024nen Boudou no Yoru | Year 2024 Night of Riot |
| 59 | Life Support | バライルの死 | Bareil no Shi | Bareil's Death |
| 60 | Heart of Stone | 可変種の定め | Kahenshu no Sadame | Destiny of Changeling |
| 61 | Destiny | 三匹の毒蛇 | Sanbiki no Dokuja | Three Poisonous Snakes |
| 62 | Prophet Motive | 新・金儲けの秘訣 | Shin Kanemouke no Himitsu | New Rules of Acquisition |
| 63 | Visionary | DS9破壊工作 | DS9 Hakai-kousaku | DS9 Sabotage |
| 64 | Distant Voices | 老化促進テレパシー | Rouka Sokushin Telepathy | Aging Acceleration Telepathy |
| 65 | Through the Looking Glass | 鏡の裏のシスコ | Kagami no Ura no Sisko | Sisko Behind Mirror |
| 66 | Improbable Cause | 姿なき連合艦隊(前編) | Sugata-naki Rengou-kantai | Vanishing Combined Fleet |
| 67 | The Die Is Cast | 姿なき連合艦隊(後編) | Sugata-naki Rengou-kantai | Vanishing Combined Fleet |
| 68 | Explorers | 夢の古代船 | Yume no Kodai-sen | Dreamy Ancient Ship |
| 69 | Family Business | クワークの母 | Quark no Haha | Quark's Mother |
| 70 | Shakaar | シャカールの乱 | Shakaar no Ran | Shakaar's Mutiny |
| 71 | Facets | クルゾンの秘密 | Curzon no Himitsu | Curzon's Secret |
| 72 | The Adversary | 忍び寄る可変種の脅威 | Shinobi-yoru Kahensyu no Kyoui | Threat of Creeping Changeling |
| No. | Original | Japanese | Romaji | Meaning |
| 73 | The Way of the Warrior, Part I | クリンゴンの暴挙(前編) | Klingon no Boukyo | Klingon's Leap in the Dark |
| 74 | The Way of the Warrior, Part II | クリンゴンの暴挙(後編) | Klingon no Boukyo | Klingon's Leap in the Dark |
| 75 | The Visitor | 父と子 | Chichi to Ko | Father and Son |
| 76 | Hippocratic Oath | 苦悩するジェム・ハダー | Kunou-suru Jem'Hadar | Groaning Jem'Hadar |
| 77 | Indiscretion | デュカットの娘 | Dukat no Musume | Dukat's Daughter |
| 78 | Rejoined | 禁じられた愛の絆 | Kinjirareta Ai no Kizuna | Ties of Forbidden Love |
| 79 | Little Green Men | フェレンギ人囚わる | Fereng-jin Torawaru | Ferengi Captured |
| 80 | Starship Down | ディファイアントの危機 | Defiant no Kiki | Crisis of Defiant |
| 81 | The Sword of Kahless | カーレスの剣 | Kahless no Ken | Sword of Kahless |
| 82 | Our Man Bashir | ドクター・ノア | Doctor Noah | Doctor Noah |
| 83 | Homefront | 地球戒厳令(前編) | Chikyu Kaigen-rei | Earth Martial Law |
| 84 | Paradise Lost | 地球戒厳令(後編) | Chikyu Kaigen-rei | Earth Martial Law |
| 85 | Crossfire | ジェラシー | Jealousy | Jealousy |
| 86 | Return to Grace | 新たなる戦線 | Aratanaru Sensen | New Battle Line |
| 87 | Sons of Mogh | モーグの息子たち | Mogh no Musuko-tachi | Sons of Mogh |
| 88 | Bar Association | ロムの反乱 | Rom no Hanran | Rom's Mutiny |
| 89 | Accession | 選ばれし者の困惑 | Erabareshi-mono no Konwaku | Emissary's Trouble |
| 90 | Rules of Engagement | 裁かれるウォーフ | Sabakareru Worf | Judged Worf |
| 91 | Hard Time | つくられた記憶 | Tsukurareta Kioku | Made Memory |
| 92 | Shattered Mirror | 鏡あわせのジェニファー | Kagami-awase no Jeniffer | Jennifer with Mirrors |
| 93 | The Muse | 二人の女神 | Futari no Megami | Two Goddesses |
| 94 | For the Cause | 裏切り者は誰だ | Uragiri-mono ha Dare da | Who Is Betrayer |
| 95 | To the Death | 戦士の宿命 | Senshi no Shukumei | Warriror's Fate |
| 96 | The Quickening | 星に死の満つる時 | Hoshi ni Shi no Mitsuru Toki | When Death Fill Planet |
| 97 | Body Parts | クワーク、絶体絶命 | Quark, Zettai-zetsumei | Quark, Do-or-die |
| 98 | Broken Link | 可変種の脅威 第二幕(前編) | Kahenshu no Kyoui Dai-ni-maku | Threat of Changeling Second Chapter |
| No. | Original | Japanese | Romaji | Meaning |
| 99 | Apocalypse Rising | 可変種の脅威 第二幕(後編) | Kahenshu no Kyoui Dai-ni-maku | Threat of Changeling Second Chapter |
| 100 | The Ship | 神の船 | Kami no Fune | God's Ship |
| 101 | Looking for Par'Mach in All the Wrong Places | クワークの再婚 | Quark no Saikon | Quark's Remarriage |
| 102 | Nor the Battle to the Strong | 戦う勇気 | Tatakau Yuki | Fighting Bravery |
| 103 | The Assignment | ケイコのために | Keiko no Tame ni | For Keiko |
| 104 | Trials and Tribble-ations | 伝説の時空へ | Densetasu no Jiku e | To Legendary Spacetime |
| 105 | Let He Who Is Without Sin... | 享楽の星・ライサ | Kyouraku no Hoshi, Risa | Planet of Pleasure; Risa |
| 106 | Things Past | 秘められた過去 | Himerareta Kako | Hidden Past |
| 107 | The Ascent | あの頂を目指せ | Ano Itadaki wo Mezase | Aim That Top |
| 108 | Rapture | 預言者シスコ | Yogensha Sisko | Prophet Sisko |
| 109 | The Darkness and the Light | 一人、また一人、そして… | Hitori, Mata Hitori, Soshite... | One, Another, and... |
| 110 | The Begotten | 幼き命 | Osanaki Inochi | Infant Life |
| 111 | For the Uniform | エディングトンの逆襲 | Eddington no Gyakushu | Eddington's Counterattack |
| 112 | In Purgatory's Shadow | 敗れざる者(前編) | Yaburezaru Mono | No-loser |
| 113 | By Inferno's Light | 敗れざる者(後編) | Yaburezaru Mono | No-loser |
| 114 | Doctor Bashir, I Presume | ジュリアンの秘密 | Julian no Himitsu | Julian's Secret |
| 115 | A Simple Investigation | オドーの恋 | Odo no Koi | Odo's Love |
| 116 | Business as Usual | 武器を売る者 | Buki wo Uru Mono | Seller of Weapon |
| 117 | Ties of Blood and Water | 父死す | Chichi Shisu | Father Dies |
| 118 | Ferengi Love Songs | 愛の値段 | Ai no Nedan | Price of Love |
| 119 | Soldiers of the Empire | 我らクリンゴン | Ware-ra Klingon | We Are Klingons |
| 120 | Children of Time | 末裔の星 | Matsuei no Hoshi | Planet of Descendant |
| 121 | Blaze of Glory | 最後のテロリスト | Saigo no Terrorist | Last Terrorist |
| 122 | Empok Nor | 眠れるステーション エムポック・ノール | Nemureru Station Empok Nor | Sleeping Station Empok Nor |
| 123 | In the Cards | プレゼント大作戦 | Present Dai-sakusen | Present Great Operations |
| 124 | Call to Arms | DS9撤退の日 | DS9 Tettai no Hi | Day of DS9 Evacuation |