- Ep: 44
- Busted
- Guest Starring: John Doe (Jeffrey Parker), Garrett M. Brown (Phillip Evans), Mary Ellen Trainor (Diane Evans), Jo Anderson (Nancy Parker), Michael Chieffo (Mr. Seligman), Phil Reeves (Judge Davis), Yorgo Constantine (Agent Burns), Jeannetta Arnette (Delores Browning)
- Co-Starring: Michael Earl Reid (Harlan), John Bisom (McGregor), Randy Thompson (Tytell), Gilbert Glenn Brown (Security Guard), Joshua Drennen (Officer)
- Written By: Jason Katims
- Directed By: Allan Kroeker
- Ep: 45
- Michael, the Guys and the Great Snapple Caper
- Guest Starring: John Doe (Jeffrey Parker), Jason Peck (Sheriff Hanson), Steven Roy (Steve), Michael Peña (Fly), Martin Starr (Monk), Earl C. Poitier (George)
- And: Terence Quinn (Carl)
- Co-Starring: Kathy Byron (Bartender), Joseph Williams (Singer)
- Written By: Ronald D. Moore
- Directed By: Paul Shapiro
- Ep: 46
- Significant Others
- Guest Starring: John Doe (Jeffrey Parker), Garrett M. Brown (Phillip Evans), Mary Ellen Trainor (Diane Evans), Jo Anderson (Nancy Parker), Michael Chieffo (Mr. Seligman), Steven Roy (Steve), Martin Starr (Monk), Michael Peña (Fly), Earl C. Poitier (George), Ivonne Coll (Mrs. Ramirez)
- And: Colin Hanks (Alex Whitman)
- Written By: David Simkins
- Directed By: Patrick Norris
- Ep: 47
- Secrets and Lies (Part 1)
- Special Guest Star: Joe Pantoliano (Kal Langley)
- Guest Starring: Stephen Tobolowsky (Julius Walters), Garrett M. Brown (Phillip Evans), Mary Ellen Trainor (Diane Evans), Bitty Schram (Bunny), Dayton Callie (Joey Ferrini), Adilah Barnes (Journalism Teacher)
- With: Stanley Anderson (James Valenti, Sr.)
- And: John Billingsley (Himself)
- Co-Starring: Eve Brent (Bess Covendall), Aimee Nicole (Actress), Barry Wiggins (Deputy Brown), Rocky McMurray (Detective Kerr), Richard Eck (Detective Erlick)
- Uncredited: Jonathan Frakes (Himself)
- Written By: Russel Friend & Garrett Lerner
- Directed By: Jonathan Frakes
- Ep: 48
- Control (Part 2)
- Special Guest Star: Joe Pantoliano (Kal Langley)
- Guest Starring: Mary Ellen Trainor (Diane Evans), Richard McGonagle (General Edward Chambers), Missi Pyle (Windy Sommers), Dylan Kussman (Brian), Julie-Anne Liechty (Blonde Woman), Ron Fassler (Scott)
- Co-Starring: Randall Rapstine (Customer)
- Written By: Gretchen J. Berg & Aaron Harberts
- Directed By: Bill Norton
- Ep: 49
- To Have and to Hold
- Guest Starring: John Doe (Jeffrey Parker), Spence Decker (Kivar), Garrett M. Brown (Phillip Evans), Mary Ellen Trainor (Diane Evans), Ivonne Coll (Mrs. Ramirez), Greg Zola (Karter)
- Co-Starring: Chad Gabriel (Mark), Danny Seckel (Richie), Benjamin Benitez (Louis), Patrick T. O'Brien (Minister), Joseph Williams (Singer)
- Written By: Ronald D. Moore
- Directed By: Fred K. Keller
- Ep: 50
- Interruptus
- Guest Starring: John Doe (Jeffrey Parker), Spence Decker (Kivar), Garrett M. Brown (Phillip Evans), Mary Ellen Trainor (Diane Evans)
- Written By: David Simkins
- Directed By: Bruce Seth Green
- Ep: 51
- Behind the Music
- Guest Starring: Clayne Crawford (Billy Darden), Mary Ellen Trainor (Diane Evans)
- And: Garrett M. Brown (Phillip Evans)
- Co-Starring: Matt Southwell (Mysterious Man)
- Written By: Russel Friend & Garrett Lerner
- Directed By: Jonathan Frakes
- Ep: 52
- Samuel Rising
- Guest Starring: Gavin Fink (Samuel Turner), Colleen Flynn (Rebecca Turner), Sean O'Bryan (Warren Turner), Navi Rawat (Shelby Prine)
- Co-Starring: Yvonne Farrow (Dr. Lynette Ramey), Allison Ward (Deb), Zachary Isaiah Williams (Zeke), Christopher Plumley (Paul), Haley King (Another Kid), Gene Borkan (Santa #1), Cole Dodson (Santa #2), Alejandro Patino (Santa #3), Bret Loehr (Kid #1), Jenevieve Norris (Kid #2)
- Written By: Jason Katims
- Directed By: Patrick Norris
- Ep: 53
- A Tale of Two Parties
- Guest Starring: John Doe (Jeffrey Parker), Eve Brent (Bess Covendall)
- Co-Starring: Frieda Jane (Bitsy), Adam Frost (Jock #1), Jason Strickland (Jock #2), Jon Ryckman (Party Guy), Scott Hamm (Boyfriend), James Ross (Daryl), Erin Foster (Susie), Melanie H. Gassaway (Karen), Frank Tignini (Frat Guy), Kimberly Russell (Girlfriend #1), Jennifer Humphrey (Girlfriend #2), Joseph Williams (Singer)
- Written By: Laura J. Burns & Melinda Metz
- Directed By: Allan Kroeker
- Ep: 54
- I Married an Alien
- Guest Starring: John Doe (Jeffrey Parker), Kristoffer Polaha (Eric Hughes), Susan Barnes (Social Worker)
- And: Garrett M. Brown (Phillip Evans)
- Written By: Ronald D. Moore
- Directed By: Patrick Norris
- Ep: 55
- Ch-Ch-Changes
- Guest Starring: John Doe (Jeffrey Parker), Meredith Scott Lynn (Dominique), Michael Chieffo (Mr. Seligman), Hal Ozsan (Adam Chase), Aki Aleong (Dr. Frank)
- Co-Starring: Michael Medico (George Winkler), Ryan Ford (Busboy), Joseph Williams (Singer)
- Written By: Gretchen J. Berg & Aaron Harberts
- Directed By: Paul Shapiro
- Ep: 56
- Panacea
- Guest Starring: Clayne Crawford (Billy Darden), Meredith Scott Lynn (Dominique), Jason Peck (Sheriff Hanson), Freda Foh Shen (Dean Hackett), Ashley Johnson (Eileen Burrows), Martin Starr (Monk Pyle)
- And: Morgan Fairchild (Meris Wheeler)
- Co-Starring: Jack Donner (Clayton Wheeler), Karl Wiedergott (Scientist)
- Written By: Russel Friend & Garrett Lerner
- Directed By: Rodney Charters
- Ep: 57
- Chant Down Babylon
- Guest Starring: Paul Fitzgerald (Paul), Ashley Johnson (Eileen Burrows)
- And: Morgan Fairchild (Meris Wheeler)
- Co-Starring: Jack Donner (Clayton Wheeler)
- Written By: Ronald D. Moore
- Directed By: Lawrence Trilling
- Ep: 58
- Who Died and Made You King?
- Guest Starring: John Doe (Jeffrey Parker), Yorgo Constantine (Agent Burns), Harry Groener (Dr. Burton Weiss)
- And: Garrett M. Brown (Phillip Evans)
- Co-Starring: Douglas Owen McDonald (Man in Black), James Oberlander (Waiter)
- Written By: Gretchen J. Berg & Aaron Harberts
- Directed By: Peter B. Ellis
- Ep: 59
- Crash
- Guest Starring: John Doe (Jeffrey Parker), Mary Ellen Trainor (Diane Evans), Woody Brown (Major Pete Carlson), Samantha Shelton (Connie Griffin), Paul Schulze (Man in Black), Larry Poindexter (Colonel Ted Griffin)
- And: Garrett M. Brown (Phillip Evans)
- Co-Starring: Lamont Thompson (Guard), Brien Blakely (Reporter), Stephen Rockwell (Scientist)
- Written By: David Simkins
- Directed By: Patrick Norris
- Ep: 60
- Four Aliens and a Baby
- Guest Starring: Emilie De Ravin (Tess Harding), Mary Ellen Trainor (Diane Evans), Woody Brown (Major Pete Carlson)
- And: Garrett M. Brown (Phillip Evans)
- Co-Starring: Gunther Jensen (Air Force Officer), Bart McCarthy (Colonel Thompson), Adrianna Banovich (Reporter), Chris Butler (Scientist), Gary Riotto (Scientist #2), Jonathan Fraser (M.P.)
- Written By: Russel Friend & Garrett Lerner
- Directed By: William Sadler
- Ep: 61
- Graduation
- Guest Starring: John Doe (Jeffrey Parker), Mary Ellen Trainor (Diane Evans), Winnie Holzman (Madame Vivian), Michael Shamus Wiles (Watcher), Patrick Kilpatrick (Watcher), Joel McKinnon Miller (Toby)
- And: Garrett M. Brown (Phillip Evans)
- Co-Starring: Taylor Young (Hannah Mills), Barry Livingston (Bryce McCain), Bob Morrisey (Principal), Brian Evers (General Wallace)
- Written By: Jason Katims & Ronald D. Moore
- Directed By: Allison Liddi-Brown
| Shiri Appleby ........ Elisabeth "Liz" Parker |  |
| Jason Behr .............. Maxwell "Max" Evans |  |
| Katherine Heigl ................ Isabel Evans |  |
| Majandra Delfino ............... Maria DeLuca |  |
| Brendan Fehr ................. Michael Guerin |  |
| Nick Wechsler .................. Kyle Valenti |  |
| Adam Rodriguez ................ Jesse Ramirez |  |
| William Sadler .................. Jim Valenti |  |
