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Dr. J. Allen Hynek
Astrophysics professor recruited by Air Force.
- Agent Mulder: Much to the disappointment of the Air Force. Initially chosen because he doubted Alien interaction with Earth, his commitment to finding the truth rather than quickly closing cases becomes a thorn in their side early on. By season's end he's chosen to be subtle about it, outwardly going along with the Air Force cover-ups so he can stay close to their cases and the truth.
- Badass Bookworm: Proves surprisingly capable of holding his own when he and Quinn come to blows, something Quinn even lampshades afterwards.
- The Cassandra: While's he flails in the dark a lot, he's show to be close to the truth at times - a lot closer than the skeptical Quinn.
- Fire-Forged Friends: He and Quinn have numerous rocky patches due to their conflicting views on exposing the truth versus covering it up - but the two are firm friends by the end of season 2, with Quinn at one point admitting Hynek is the only one he trusts.
- Secret Keeper: He has to keep the Air Force's investigations into UFOs secret - but also keeps the existence of the Man in Black helping him secret until Quinn figures it out in the first season finale.
- Shut Up, Hannibal!: Gives Wernher Von Braun this when the German tries to appeal to his scientist background, angrily accusing him of being a serial liar who sacrificed his scientific principles for glory.
- Teeth-Clenched Teamwork: Ends up working with the Men in Black's leader William Fairchild, despite his massive distrust of him, to find the disappeared Quinn at the end of season 2.
Captain Michael Quinn
US Air force captain
- Ace Pilot: Served as a fighter pilot in World War 2, and is still one in the present day. "Broken Arrow" mentions he has six commendations for valour.
- Agent Scully: Just wants to close cases and not piss off his superiors. Even when he starts to question the validity of their work, his assumption is Russians. Subverted at the end of season 1: dogfighting a UFO and realising how far advanced it is beyond his jet causes him to at least believe it's not anything human.
- Backstory of the Day: His being one of the first into Buchenwald only comes up when they have to deal with actual ex-Nazi scientists.
- Berserk Button: He was one of the first Americans into Buchenwald concentration camp, and consequently loathes the idea of America employing ex-Nazi scientists like Wernher Von Braun - it almost gets him fired in "Operation Paperclip".
- Dating Catwoman: With Susie, though he doesn't know it.
- I Need a Freaking Drink: It's a rare episode in season 1 that doesn't feature him sitting at his desk downing whisky at some point near the end.Quinn (after seeing a film showing an alien autopsy): How about you tell me if there's any goddamn bourbon in the house and we'll go from there.
- Inferred Survival: Disappears after the Navy depth charge him and the underwater UFOs he's investigating, but Hynek's absolutely sure he survived.
- Just Following Orders: His usual excuse for trying to shut down their cases. More justified than most examples of this trope, as unlike Hynek he's a standing US Air Force officer and not doing what his superiors (who he has to deal with directly) say could cost him promotion or even his job. Gets it thrown back in his face in "Close Encounters" when Banks, after almost ruining their reputation in front of the Robertson Panel, claims to have been doing this with respect to the CIA - something Quinn grudgingly admits to understanding.
- Skeptic No Longer: Let's just say he doesn't have the best time of it in season 2.
Dr Hynek's wife of 12 years
- Housewife: Fits the mould perfectly.
- Locked Out of the Loop: Hynek keeps her in the dark about what he's doing - which both makes it easy for Susie to manipulate her, and actually sets him back when the deranged Henry Fuller turns up needing to talk with him and she has no idea what he's talking about. Averted in season 2, where he uses her to uncover information on his cases from UFO groups.
- Spanner in the Works: Her stealing classified files from the Air Force almost ruins Blue Book, and leads Susie to expose her true nature as a spy to save her and Quinn.
- Unwitting Pawn: Of Susie in season 1.
- Action Mom: Turns out to have a daughter in season 2, and murders Rizzuto to keep her safe.
- Becoming the Mask: Her assignment is to gain Mimi's trust to find out what her husband knows - but she grows increasingly fond of Mimi, and almost blows her own cover saving her from the deranged Fuller.
- The Cast Showoff: Ksenia Solo really can speak fluent Russian.
- Femme Fatale Spy: A Soviet deep-cover spy perfectly capable of seducing her target, and willing to kill at the drop of a hat.
- I Have Brothers: Averted, but alluded to as she mentions her father always wanted sons to explain how she can help Mimi build her bomb shelter.
- Klingon Promotion: Kills her own superior after he both takes too many liberties with her and tries to take her off the Blue Book assignment.
- Sensual Slav: She's played by Ksenia Solo. No wonder Mimi and Quinn fall for her. Amusingly backfires after killing Rizzuto when she claims to be his girlfriend, as Harding is instantly suspicious that he'd even know anyone anywhere near that attractive.
- Uncertain Doom: Allows herself to be arrested and take the blame for the stolen files to protect Quinn and Mimi. As a Soviet spy, her real-world fate would likely be execution, and she certainly thinks so given that she gives Mimi her last letter to her daughter - but the second season ends without showing her fate.
- You Have Outlived Your Usefulness: Her superiors try to do this to her after she refuses to have Quinn kidnapped. Unusually, she survives and manages to buy her own life by killing another Soviet agent who'd defected to the Americans.
Played By: Neal McDonough
- Bad Boss: His threatening to demote/fire Quinn (and frequently Hynek) if they don't produce results to his liking is a fairly regular occurrence.
- Berserk Button: Don't call him a coward.
- Everyone Has Standards: He regards himself as a patriot first and foremost, so he's genuinely shocked and furious when he discovers the Secretary of Defence was involved in testing fear gas on American soldiers. Later, when an intelligence sting goes wrong, he personally steps in to save their operative, contrasting Valentine who's only worried about getting caught.
- I Did What I Had to Do: His rationale for his many shady actions. At one point he draws a direct comparison between what he's doing and the Hiroshima bombing, claiming that sometimes doing the unthinkable is necessary to stave off a greater tragedy.
- A Lighter Shade of Black: He's intimidating and ruthless, but he's definitely not as bad as his compatriot Valentine.
- Oh, Crap!: When he realises he's been tricked into playing a film seemingly showing the existence of alien life on nationwide TV.
- Spotting the Thread: When he visits his Double Agent Rizzuto and finds Susie (who's just killed him) claiming to be his girlfriend, he's instantly suspicious that Rizzuto would even know anyone that attractive, never mind have a girlfriend like her.
- Villainous Breakdown: Throughout the Roswell two-parter and after; he was the main mover-and-shaker in covering up what happened, and having to return to the town when things start to go wrong drives him to steadily more irrational behaviour, including waterboarding non-compliant townsmen, seriously impairing his judgment through ill-advised drinking and almost getting exposed on live TV. After, he's shown visiting a confessional to try and reconcile the things he's seen with his religious beliefs, and is clearly having a tough time holding it together.
- Well-Intentioned Extremist: His continual denial of alien life leads him to lie to the American public, and almost starts a war with the Russians at the end of season one, but season 2 shows he genuinely believes the whole thing is a Russian conspiracy, and that he's protecting the world by doing this.