Walter is the game's main male protagonist. Walter first experiences the realities of war in the First Huffman War, which inspires him to enlist in the USN Army. In the Second Huffman War, Walter encounters his former best friend Glen Duval on three separate occasions. After the war, he applies to join the Strike Wyverns, which sets in motion the events that lead to more encounters with Glen. Over the years, Feng works very hard in military operations, gaining the respect of his colleagues and superiors. While he is a patriot, Feng is conflicted between following his moral code or the USN's on many occasions. Walter refuses to be implanted with the Type-S device after he joins the Barghest unit. While this puts him at a major disadvantage in battles against Type-S users, Walter constantly trains to refine his piloting skills. As a result, Walter is one of the very few normal pilots in the world who can survive encounters against Type-S users.
Lynn is the game's main female protagonist. Lynn's military history includes graduating from the Home 47 division and serving in the Barghest unit. Upon leaving the Barghest for undisclosed reasons, she assumes command of the Strike Wyverns unit. She is well known for her always-serious and demanding attitude, despite having a soft spot for Walter. Every Marine in the Strike Wyverns obey her out of fear of being sent to the "Kill House", a location where she deals with disobedient soldiers. Over time, Wenright falls in love with Walter and the two eventually get married. Their daughter, who resembles Lynn, is shown in the epilogue.
Glen is another childhood friend of Walter and Randy. During a skirmish in the First Huffman War, Glen protected Walter from bullet casings fired by a nearby Wanzer (which is how they received their scars). When Randy and Walter enlisted in the USN Army, Glen did not join them and enlisted in the OCU Army instead. Glen encounters both of them on three separate occasions in the future, killing Randy on the third encounter. Since the Fort Monus City experience, Glen and Walter have crossed paths in the future around the world. Through intelligence reports, it is revealed that Glen works for the Grimnir and is now a Type-S user, though he suffers from the device's worst condition, losing all the memories of his life before working for Grimnir. Despite this, Glen masters the device's abilities and later upgrades to the revised Type-S Device, making him one of the deadliest Wanzer pilots in the world.
Randy is a childhood friend of Walter and Glen, growing up together in Freedom City. Randy's decision to enlist in the USN Army was influenced by the scars that Walter and Glen received during a skirmish in the First Huffman War. Walter and Randy trained at the Home 47 division and later served in the infantry, though Randy desired to become a Wanzer pilot. Though a nice and pleasant person, O'Neill rarely comes across as reliable in regards to military work. Despite his apparent capriciousness, he has a strong sense of right and wrong and he loathes unfair play. A chocolate lover, he keeps a candy bar in his front pocket at all times. He is killed during a skirmish in Fort Monus City after Glen fires a shotgun round directly into his Wanzer's cockpit.
Edward is an acquaintance of Walter's and acts as a squadron leader for the Strike Wyverns unit. Edward enlisted in the USN Army and studied at Home 47, which is where Walter, Randy, and Lynn received military training. After an undisclosed period of time, Edward applies and gets accepted into the Strike Wyverns unit. He is good friends with Walter and Lynn, although the latter is particularly annoyed at his personality. Edward's personality is described with the quote, "Even speaking to him once in three years is more than enough." Edward therefore loves chatting, and gives everyone a headache except for Walter. Collins enjoys exercising when off-duty, though he views Wanzer piloting as a form of exercise as well.
Hector is a Lieutenant Colonel and the leader of the elite Barghest unit. Reynolds' military history is unknown, though it is documented that he was a test subject for the Type-S Device. Hector and Lynn once worked together in the Barghest unit, but Wenright dislikes working with him for undisclosed reasons. This is evident when she attempts to shoot Hector during an operation to eliminate the Hawkes terrorist group. Since the Barghest unit specializes in anti-terrorism, Hector has plenty of connections worldwide to gather data on terrorist activities. He is heavily involved with gathering data on the Grimnir terrorist group and its elusive leader, Morgan Bernard.
One of the protagonists in Front Mission 3, Emir is the head researcher of a new radiation-based technology known as MIDAS. Klamsky is assigned to the USN Alaska Special Radiation Laboratory to research and complete the system. Although the initial purpose of the project was to develop a new source of clean energy, Emir is not pleased when the USN Army wants to turn it into a weapon. Walter and Hector become good friends with Emir despite knowing that she is a product of the Imaginary Number project. Through conversations, Emir reveals the existence of the original MIDAS: Mass Interparticle Dissociation Antiproton Synthesizer. This MIDAS operates differently from the one in Front Mission 3, which was a prototype version of the system, as Emir states.
Morgan is the creator of the Type-S Device and the leader of the Grimnir terrorist organization. Aside from this, very few details are known about him. The Grimnir is the most feared terrorist organization in the world, having major influences and connections in all continental superstates. Though initially concentrated in EC and OAC nations, the Grimnir eventually expanded operations to territories in the USN, OCU, and the Republic of Zaftra. All world powers have attempted to eradicate the organization, but these attempts have largely failed. Many who have encountered the Grimnir end up either missing or dead, making it difficult to gather information on them.