| Title | Season Episode | Airdate | Stardate | Year | Rating | |
| Equinox, Part 2 | 6 x 01 | 121 | 22 Sep 1999 | Unknown | 2376 |  |
| Survival Instinct | 6 x 02 | 122 | 29 Sep 1999 | 53049.2 | 2376 |  |
| Barge of the Dead | 6 x 03 | 123 | 6 Oct 1999 | Unknown | 2376 | |
| Tinker, Tenor, Doctor, Spy | 6 x 04 | 124 | 13 Oct 1999 | Unknown | 2376 |  |
| Alice | 6 x 05 | 125 | 20 Oct 1999 | Unknown | 2376 | |
| Riddles | 6 x 06 | 126 | 3 Nov 1999 | 53263.2 | 2376 |  |
| Dragon's Teeth | 6 x 07 | 127 | 10 Nov 1999 | 53167.9 | 2376 | |
| One Small Step | 6 x 08 | 128 | 17 Nov 1999 | 53292.7 | 2376 | |
| The Voyager Conspiracy | 6 x 09 | 129 | 24 Nov 1999 | Unknown | 2376 | |
| Pathfinder | 6 x 10 | 130 | 1 Dec 1999 | Unknown | 2376 | |
| Fair Haven | 6 x 11 | 131 | 12 Jan 2000 | Unknown | 2376 | |
| Blink of an Eye | 6 x 12 | 132 | 19 Jan 2000 | Unknown | 2376 | |
| Virtuoso | 6 x 13 | 133 | 26 Jan 2000 | 53556.4 | 2376 | |
| Memorial | 6 x 14 | 134 | 2 Feb 2000 | Unknown | 2376 | |
| Tsunkatse | 6 x 15 | 135 | 9 Feb 2000 | 53447.2 | 2376 | |
| Collective | 6 x 16 | 136 | 16 Feb 2000 | Unknown | 2376 |  |
| Spirit Folk | 6 x 17 | 137 | 23 Feb 2000 | Unknown | 2376 | |
| Ashes to Ashes | 6 x 18 | 138 | 1 Mar 2000 | 53679.4 | 2376 | |
| Child's Play | 6 x 19 | 139 | 8 Mar 2000 | Unknown | 2376 | |
| Good Shepherd | 6 x 20 | 140 | 15 Mar 2000 | 53753.2 | 2376 | |
| Live Fast and Prosper | 6 x 21 | 141 | 19 Apr 2000 | 53849.2 | 2376 | |
| Muse | 6 x 22 | 142 | 26 Apr 2000 | 53896 | 2376 | |
| Fury | 6 x 23 | 143 | 3 May 2000 | Unknown | 2376 | |
| Life Line | 6 x 24 | 144 | 10 May 2000 | Unknown | 2376 | |
| The Haunting of Deck Twelve | 6 x 25 | 145 | 17 May 2000 | Unknown | 2376 | |
| Unimatrix Zero, Part 1 | 6 x 26 | 146 | 24 May 2000 | Unknown | 2376 | |
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