| Season One | 13 animated color episodes in 30 minute format | |||
|---|---|---|---|---|
| Ep | PN | Airdate | Title | |
| 1 | 1 | Jan 10/99 | Rebirth | |
| 2 | 2 | Jan 10/99 | Rebirth, Part 2 | |
| 3 | 3 | Jan 30/99 | Black Out | |
| 4 | 4 | Feb 06/99 | Golem | |
| 5 | 7 | Feb 13/99 | Meltdown | |
| 6 | 8 | Feb 20/99 | Heroes | |
| 7 | 10 | Mar 13/99 | Shriek | |
| 8 | 6 | Mar 20/99 | Dead Man's Hand | |
| 9 | 5 | Apr 10/99 | The Winning Edge | |
| 10 | 9 | May 01/99 | Spellbound | |
| 11 | 12 | May 08/99 | Disappearing Inque | |
| 12 | 11 | May 15/99 | A Touch of Curaré | |
| 13 | 13 | May 22/99 | Ascension | |
| Season Two | 26 animated color episodes in 30 minute format | |||
|---|---|---|---|---|
| Ep | PN | Airdate | Title | |
| 14 | 16 | Sep 17/99 | Splicers | |
| 15 | 15 | Sep 25/99 | Earth Mover | |
| 16 | 14 | Oct 02/99 | Joyride | |
| 17 | 17 | Oct 09/99 | Lost Soul | |
| 18 | 19 | Oct 16/99 | Hidden Agenda | |
| 19 | 18 | Oct 23/99 | Bloodsport | |
| 20 | 20 | Nov 06/99 | Once Burned | |
| 21 | 21 | Nov 13/99 | Hooked Up | |
| 22 | 22 | Nov 20/99 | Rats | |
| 23 | 23 | Dec 04/99 | Mind Games | |
| 24 | 24 | Dec 11/99 | Revenant | |
| 25 | 25 | Jan 08/00 | Babel | |
| 26 | 26 | Jan 15/00 | Terry's Friend Dates a Robot | |
| 27 | 27 | Jan 22/00 | Eyewitness | |
| 28 | 30 | Feb 05/00 | Final Cut | |
| 29 | 29 | Mar 04/00 | The Last Resort | |
| 30 | 31 | Mar 11/00 | Armory | |
| 31 | 32 | Mar 25/00 | Sneek Peek | |
| 32 | 34 | Apr 01/00 | The Eggbaby | |
| 33 | 28 | Apr 08/00 | Zeta (Basis for The Zeta Project) | |
| 34 | 33 | Apr 15/00 | Plague | |
| 35 | 35 | Apr 22/00 | April Moon | |
| 36 | 37 | May 06/00 | Sentries of the Last Cosmos | |
| 37 | 36 | May 13/00 | Payback | |
| 38 | 40 | May 27/00 | Where's Terry? | |
| 39 | 41 | Aug 19/00 | Ace in the Hole | |
| Season Three | 13 animated color episodes in 30 minute format | |||
|---|---|---|---|---|
| Ep | PN | Airdate | Title | |
| 40 | 42 | Sep 16/00 | King's Ransom | |
| 41 | 39 | Sep 23/00 | Untouchable | |
| 42 | 46 | Sep 30/00 | Inqueling | |
| 43 | 38 | Oct 07/00 | Big Time | |
| 44 | 44 | Oct 21/00 | Out of the Past | |
| 45 | 45 | Nov 04/00 | Speak No Evil | |
| 46 | 50 | Nov 11/00 | The Call | |
| 47 | 51 | Nov 18/00 | The Call, Part 2 | |
| 48 | 43 | Dec 09/00 | Betrayal | |
| Dec 12/00 (DTV) | Batman Beyond: Return of the Joker (76 mins) | |||
| 49 | 48 | Feb 03/01 | Curse of the Kobra | |
| 50 | 49 | Feb 10/01 | Curse of the Kobra, Part 2 | |
| Apr 07/01 | Shadows (The Zeta Project episode) | |||
| 51 | 52 | Apr 07/01 | Countdown (The Zeta Project crossover) | |
| 52 | 47 | Dec 18/01 | Unmasked | |
| Apr 27/02 | Ro's Gift (The Zeta Project episode) | |||
| Jan 29/05 | The Once and Future Thing, Part Two: Time, Warped (Justice League Unlimited episode) | |||
| Jul 23/05 | Epilogue (Justice League Unlimited episode) | |||
