| Ep. # | Episode Title | Filming Schedule | Airdate | Lead Time |
| 053 |
"The Xindi" | Filming from June 26 to July 9 (early morning July 10).
No filming July 4 (Independence Day).
Nine-day shooting schedule. | 9/10/03 | 61 days |
| 054 |
"Anomaly" | Filming from July 10 to 18. | 9/17/03 | 59 days |
| 055 |
"Extinction" | Filming from July 21 to 29. | 9/24/03 | 56 days |
| 056 |
"Rajiin" | Filming from July 30 to August 7.
Second-unit filming on August 8 and one day the following week.
Working title "Enemy Advances". | 10/01/03 | 54 days |
| 057 |
"Impulse" | Filming from August 8 to 20 (overlap with "Exile"). | 10/08/03 | 48 days |
| 058 |
"Exile" | Filming from August 20 (overlap with "Impulse") to 29 (overlap with "The Shipment"). |
10/15/03 | 46 days |
| 059 |
"The Shipment" | Filming from August 29 (overlap with "Exile") to September 9.
No filming September 1 (Labor Day). |
10/29/03 | 49 days |
| 060 |
"Twilight" | Filming from September 10 to 19.
Filming shut down on September 15 in memory of First Assistant Director Jerry Fleck.
Second-unit photography on 10/13 (overlap with "Similitude" and "Carpenter Street"). |
11/05/03 | 46 days |
| 061 |
"North Star" | Filming from September 22 to 30.
Includes location shooting from September 23 to 29.
Second-unit photography on 10/1 (overlap with "Similitude"). |
11/12/03 | 41 days |
| 062 |
"Similitude" | Filming from October 1 (overlap with "North Star") to 9.
Second-unit photography on 10/13 (overlap with "Twilight" and "Carpenter Street"). |
11/19/03 | 40 days |
| 063 |
"Carpenter Street" | Filming from October 10 to 20 (overlap with "Twilight" and "Similitude" on 10/13).
Includes location shooting from October 14 to 17.
Second-unit photography on 10/21-22 (overlap with "Chosen Realm"). |
11/26/03 | 34 days |
| 064 |
"Chosen Realm" | Filming from October 21 to 29 (overlap with "Carpenter Street" on 10/21-22).
Second-unit photography the week of December 8-10 (overlap with "Proving Ground" and "Doctor's Orders"). |
01/14/04 | 76 days |
| 065 |
"Proving Ground" | Filming from October 30 to November 7.
Second-unit photography the week of December 8-10 (overlap with "Chosen Realm" and "Doctor's Orders"). | 01/21/04 | 74 days |
| 066 |
"Strategem" | Filming from November 10 to 18. | 02/04/04 | 77 days |
| 067 |
"Harbinger" | Filming from November 19 to December 1.
No filming November 27-28 (Thanksgiving).
Second-unit photography on 12/2 (overlap with "Doctor's Orders"). | 02/11/04 | 70 days |
| 068 |
"Doctor's Orders" | Filming from December 2 (overlap with "Harbinger") to 10
(overlap with "Proving Ground" and "Chosen Ground" the week of December 8-10).
Second-unit photography on January 23 (overlap with "Hatchery", "Damage", and "The Forgotten"). |
02/18/04 | 68 days |
| 069 |
"Hatchery" | Filming from December 11 to 19.
Second-unit photography on January 23 (overlap with "Doctor's Orders", "Damage", and "The Forgotten"). | 02/25/04 | 66 days |
| 070 |
"Azati Prime" | No filming December 22 to January 2 (Christmas vacation).
Filming from January 5 to 14 (overlap with "Damage" on January 13 and 14). |
03/03/04 | 48 days |
| 071 |
"Damage" | Filming from January 13 to 22 (overlap with "Azati Prime" on January 13 and 14).
Second-unit photography on January 23
(overlap with "Doctor's Orders", "Hatchery", and "The Forgotten"). |
04/21/04 | 89 days |
| 072 |
"The Forgotten" | Filming from January 23 (overlap with "Doctor's Orders", "Hatchery", and "Damage") to February 2.
Second-unit photography on February 3 (overlap with "E²"). |
04/28/04 | 85 days |
| 073 |
"E²" | Filming from February 3 (overlap with "The Forgotton") to 11.
Second-unit photography on February 13 (overlap with "The Council") and
March 8 (overlap with "Countdown" and "Zero Hour"). |
05/05/04 | 83 days |
| 074 |
"The Council" | Filming from February 12 to 23 (overlap with "E²" on February 13).
No filming February 16 (President's Day).
Second-unit photography on February 26 (overlap with "Countdown"). |
05/12/04 | 78 days |
| 075 |
"Countdown" | Filming from February 24 to March 4 (overlap with "The Council" on February 26).
Second-unit photography on March 8 (overlap with "E²" and "Zero Hour"). |
05/19/04 | 75 days |
| 076 |
"Zero Hour" | Filming from March 5 to 16 (overlap with "E²" and "Countdown" on March 8). Season finale. |
05/26/04 | 70 days |