- Voiced by: Hideyuki Tanaka
The main protagonist. He was one of the five "Policenauts" tasked with upholding the law on Beyond Coast until an accident sends him drifting in space for 25 years. He now works as a private detective in Los Angeles and is hired by his ex-wife Lorraine to help find her missing husband Hojo. Following her murder at the hands of a masked motorcyclist, Jonathan travels to Beyond Coast and meets with his former partner Ed to solve the mysteries behind Hojo's sudden disappearance.
- Expy: Is clearly based on Martin Riggs.
- Handsome Lech: Jonathan simply cannot keep his eyes or hands to himself when he's around good-looking women. While most women will call him out on it, Meryl allows him to indulge himself if he can beat her shooting range score, and Chris has no problem whatsoever.
- Human Popsicle: His EMPS accident or rather sabotage left him in a cryogenic life pod for 25 years.
- Private Detective: Since the Policenauts and LAPD had moved on while he was still in his life pod, he had to settle for handling missing-persons cases for hire.
- Smoking Is Cool: He's almost never seen without a cigarette in his mouth, although it's rarely lit. He's also vehement on using "real" cigarettes when everyone else has switched over to "bent" cigarettes that give off no secondhand smoke.
- Voiced by: Shozo Iizuka
One of the five "Policenauts" and Jonathan's former partner. He now works as the chief of Beyond Coast Police's Vice Unit and is a devoted father to his two children, Anna and Marc. He rejoins Jonathan to help solve the mysteries behind Lorraine's murder and Hojo's disappearance.
- Doesn't Like Guns: Thanks to a traumatic incident in the past, he's unable to use a gun. He gets over it in time for the climax.
- Expy: Based on Roger Murtaugh, with a bit of Sgt. Al Powell for good measure.
- Friend on the Force: Since Jonathan's a private detective and no longer an actual policeman, Ed has to handle the official business.
- The Lost Lenore: His wife died of a kidney stone some time before the events of the game.
- Manly Tears: At the end, when Marc finally accepts him as a father.
- Not So Above It All: While he usually scolds Jonathan's Handsome Lech behavior, he sometimes indulges in it himself, only to cut himself off.
- Voiced by: Kikuko Inoue
A news reporter on Beyond Coast, she is the daughter of Lorraine and Kenzo Hojo. She bears a striking resemblance to her mother.
- Hot Scoop: A drop-dead gorgeous news anchor.
- Ill Girl: She was diagnosed with secondary aplastic anemia, and is waiting for a bone marrow transplant.
- Show Within a Show: Her news program updates several times during the game, even when she's sick at home.
- Voiced by: Kaneto Shiozawa
A member of BCP's Advanced Police Unit, he is a "Frozener", a race of artificially conceived humans possessing genes best suited for outer space. He is also an expert EMPS pilot.
- Ace Pilot: He's an expert EMPS pilot, which earned him the nickname "Mr. Goddard", after his EMPS suit.
- Artificial Human: A "Frozener", made from cryogenically preserved eggs and sperm and implanted in a surrogate mother (Chris, in Tony's case) on behest of the government, not unlike Les Enfantes Terribles.
- Badass Biker: He rides a sleek motorcycle when on assassination duty, and he's not only an excellent rider, but also a ride-by shooter.
- Better to Die than Be Killed: When Jonathan finally catches him after a long chase up Tokugawa's HQ, Tony jumps off a railing to his death to deny Jonathan the satisfaction of killing him.
- Demolitions Expert: His official role in the Advanced Police. He's just as good at setting bombs as he is at disposing of them; he manages to kill Lorraine with a car bomb and Dave with a handbag bomb.
- The Dragon: To Gates and Tokugawa.
- Evil Laugh: When gunning down Chris, and later when he throws himself to his death.
- Killer Cop: Most certainly a bad guy/cop in Beyond when he's needed by Gates/Tokugawa to keep their hands clean in killing unwanted people.
- Made of Iron: Tony is very, very hard to kill. During the first gunfight alone, he survives numerous gunshot wounds, writes out a death threat in his own artificial blood, rides a motorcycle despite a massive wound in his right wrist, and still returns to work almost immediately after with little issue. No wonder the villains use him as their attack dog.
- Obviously Evil: Jonathan suspects him of killing Lorraine almost immediately after meeting him, and he's right.
- Professional Killer: He's the Big Bad Duumvirate's personal hitman, killing Lorraine, Dave, Chris, and Ishida on their behalf.
- Villain with Good Publicity: Tony's publicly known as a APU officer.
- Voiced by: Osamu Saka
Another one of the "Policenauts", he is now the chief of BCP and commander of the AP unit, giving him the highest police authority in Beyond Coast.
- Big Bad Duumvirate: Along with Tokugawa.
- Badass Beard: Sports an impressive white chin curtain. Considering his role in the Big Bad Duumvirate, it's also a Beard of Evil.
- By-the-Book Cop: As expected of Da Chief, complete with Bothering by the Book to hamper the heroes' investigations into Tokugawa and the BCP.
- Da Chief: Head of the Advanced Police, and BCP in general. He's also a Reasonable Authority Figure, or so it would seem.
- Dirty Cop: His true nature.
- Evil Brit: Scotland Yard's representative among the Policenauts, and one of the main villains.
- Evil Laugh: He and Tokugawa chortle menacingly to themselves after framing and arresting Jonathan for murder.
- A God Am I: Gives this vibe during his Motive Rant to Jonathan in the climax, claiming that he and Tokugawa are doing God's work with the use of smuggling organs.
- Miranda Rights: Recites these to Jonathan when he is arrested for Kenzo's murder.
Joseph Sadaoki Tokugawa
- Voiced by: Iemasa Kayumi
One of the "Policenauts". After quitting from BCP, he took over his family's company, the Tokugawa Group, and soon became the most powerful figure on Beyond, even wielding influence over the colony's media. He is also the chairman of ISPA, the International Space Promotion Agency, Beyond's space development project.
- Big Bad Duumvirate: With Gates.
- Corrupt Corporate Executive: In the extreme. For example, the launch party for his company's latest drug delivery system includes escorts cloned from dead celebrities and his own DNA, at least three different crime lords, and a military-grade EMPS stationed in a corner. His secret operations are even worse.
- Evil Laugh: When Jonathan is arrested for murder, he and Gates chortle menacingly to themselves.
- I Own This Town: Tokugawa and his corporation have their hands in everything, from Beyond Coast Central Hospital to the International Space Promotion Agency (of which he is president) to a facility on the Moon that contains his organ-cloning operation. He even offered to outright buy the Beyond Coast Police department.
- Voiced by: Masaharu Sato
One of the five "Policenauts" who now serves as head of security at Tokugawa's Moon Plant.
- Make It Look Like an Accident: As it turns out, Jonathan's accident was no accident at all, since he was the one who sabotaged Jonathan's EMPS under orders from Tokugawa.
- Voiced by: Kyoko Terase
A member of BCP's vice unit who was originally a soldier for the High Tech Special Forces Unit FOXHOUND, but after the unit disbanded, she began living in Beyond.
- Best Her to Bed Her: She's one of the few women in the game who allows Jonathan to feel her up, but only if he beats her high score in a shooting range minigame.
- Continuity Snarl: Only in hindsight. She is described as participating in the fall of Zanzibarland, but is a rookie in her actual debut, Metal Gear Solid, released three years after Policenauts. Her role was originally intended for Solid Snake.
- Voiced by: Bin Shimada
Meryl's partner in the BCP Vice Unit. Unlike Meryl, he is a pacifist who dislikes violence and prefers to apprehend criminals by shooting them in the limbs rather than vital spots. Despite their differences, they get along really well. He is also a fan of junk food.
- Big Eater: He loves to eat, and is often shown eating a hamburger.
- Eyes Always Shut: And they briefly open when he dies.
- Goggles Do Nothing: Wears goggles over his head and never puts it on.
- Sacrificial Lion: He is killed by Redwood at the end of Act 2.
- Trademark Favorite Food: Hamburgers.
- Voiced by: Chiyoko Kawashima
Jonathan's ex-wife who remarried Kenzo after Jonathan's disappearance 25 years ago and also gave birth to their daughter Karen. After her husband's disappearance, she hires Jonathan to help find him, only to be murdered outside Jonathan's office.
- Small Role, Big Impact: Her murder in downtown (Old) Los Angeles is what sets Jonathan's investigation into who ordered her death.
- Voiced by: Chiyoko Kawashima
The director of BCCH (Beyond Coast Central Hospital). She was originally a teenage role model and became acquainted with the Policenauts after posing with them on a magazine cover.
- "Basic Instinct" Legs-Crossing Parody: Her pose when she first meets Jonathan and Ed in her office.
- Sickbed Slaying: Tries to kill Ed after he is hospitalized late in the game.
- Voiced by: Yumi Touma
Ed's teenage daughter and university student who attends UCBC (University of California at Beyond Coast). After Ed's wife Catherine had died, she took over all household duties.
- Voiced by: Junko Hagimori
Ed's adoptive son. Marc lost his real parents after his biological father went crazy and stabbed his wife to death and Ed was left with no choice but to shoot him in an act of self-defense. As a result of this incident, Marc was left mute.
- Ambiguous Disorder: Following his traumatic past, he seems to have developed one of these. It's implied to be autism.
- Cute Mute
Lorraine's current husband who works as the head of Tokugawa's Drug Delivery System Development Team. Following his disappearance, Lorraine hires Jonathan to help find him.
- Voiced by: Kohei Miyauchi
A forensic scientist at BCP, originally from the Soviet Union. He uses a machine called AID (Auto-analysis Identification Device) for his research.
- Voiced by: Naoki Tatsuda
The pharmacist who is in charge of BCCH's pharmacy.
- Voiced by: Nobutoshi Canna
A receptionist and security guard at Tokugawa Pharmaceuticals.