He ate too much baked beans for dinner. The gas was too much for his closed suits air filtration to clear and so he died from suffocation
SpartanQ82, I just want to let you know that your wrong, no matter how little you justify yourself. Legendary edition commentary confirms that Jun is still alive.everyone i just want to let you know, jun is dead. no matter how you justify yourself, he is. all of the first two spartan III classes are dead. and everyone but jorge is a spartan III. they were only given downgraded MJOLNIR armor.
gaaaaaaaaaaaaahhhh!!!after escaping halsey's lab, jun and the doctor landed on a leveled city, with nearly no human or covenant occupents with the exception of a lone elite. Upon sighting the elite, jun threw the doctor to the ground and kneeled, lining up the crosshairs with the creatures left eye. Breathing out, jun slowly squeezed the trigger, and time slowed. Jun took a glance at the doctors dirty face, teary eyed and full of despair, and focused his attention back on the elite. The bullet flew straight and drilled through the elite's eye, forcing the creature off it's feet and nearly five feet backwards. The creature rolled along the concrete and then slammed into a metal street sign bending it's foundation. It ceased to move. Jun drew his knife, and crept towards the creature. It lay motionless on the concrete, so jun turned and helped the doctor up. But farther off in the distance he saw something. It was a massive structure gliding in the air with two forward facing prongs. It was a covenant escort vehicle, dropping off a large squad of atleast twenty enemy infantry. Six elites, eight grunts, and six brutes. Jun took the doctors hand and quickly pulled her inside of the closest still standing building. Jun sat, silent, cleaning his gun and reloading his ammunition. Nearly twenty minutes later, he silently peered around the corner and noticed the enemy patrol examining the body of the dead elite. Halsey stood, but tripped and kicked a small metal object making a loud crash. The entire enemy patrol forced their attention directly towards jun and fired. Two shots rang off, one striking jun in the left forearm. Jun leapt back clutching the purple needle stuck through his forearm. Unfortunate. It struck both his shooting arm and his tacpad, cutting off his communication to any remaining human resistance. Jun dropped his gun and took up and ambush position, drawing his knife. The first three grunts slowly walked in the building. Jun grapped the first by the mouth, plunging the knife through it's right eye and out the back of it's skull, then swung it's body around knocking the other two grunts off it's feet. Jun lifted one up by the throat and sent it flying towards the wall, spearing it on a piece of exposed piece of rebar. The third grunt fired a plasma burst but missed by a hair, giving jun time to send his fist straight through the creatures armor, making contact with it's fleshy stomach, severing it's spinal cord. Jun quickly grabbed his knife, turned as an elite jumped into the building, and threw it, straight into the creatures throat. Jun ripped his knife out and grabbed the creatures plasma rifles and fired at the other five grunts taking them each down fast with several shots, each making contact with the creatures skulls. Jun pulled the piece of exposed rebar out of the wall and slammed it through the first brutes skull. He gripped the brutes grenade and threw it between the patrol. The remaining brutes were killed, along with two of the elites. The other three elites sprinted straight at jun, discarding their guns and drawing their energy swords. The first elite leapt at jun and sliced the air directly over his head, giving jun time to retaliate, kicking the creature directly in the stomach, grabbed it's sword, and stabbed it through the chest. The next two elites ran towards him, swords drawn. Jun blocked the creatures sword attack, and his fist made contact with it's face, sending it backwards, and he turned fast and sliced the chest armor of the creature, but making no physical damage. The elite kicked jun in the stomach sending him on his back, but jun still held the sword. Jun rolled backwards, picked up his knife laying on the floor and threw it at the creature stabbing it in the left shoulder causing it to drop it's sword. Jun leapt forward and pounced on the elite, grabbing it's other sword, and stabbing it through the chest. But a deep roar penetrated the air and caused jun to turn, just as the bottom of an elite's boot made contact his face, sending him crashing through the concrete wall. But jun was fast and immediately jumped back onto his feet, swords hand. The elite slowly circled him, taunting him with various clicks and growls. Halsey screamed, gaining the elite's full attention, giving jun time to shove both swords into the creatures kneck and with a sick twisting motion, the elite's head rolled off of it's shoulders and to the floor. The dead hands flew up and felt the air around where it's head used to be, before collapsing to the ground with several spasomadic jerks. Jun sprinted up the stairs towards halsey, but another elite pounced on him. This certain elite was familiar. It appeared to have a deep bullet wound in it's left eye. Then jun remembered. He hadn't killed this elite with that bullet. Only knocked it unconcious. The elite gave a wry smile and threw jun's swords to the other side of the room and jerked it's arms forward, causing two energy-sword like assassination blades to creep out of it's armor forearms. It slowly raised up and picked jun off his feet by the throat. It seemed to stand there and taunt jun for a few minutes before sending it's blade straight through jun's torso, severing his spinal cord, breaking every rib, and killing him instantly. But the creature broke it's attention on halsey who jumped on it's back and stabbed it in the top of the helmet with an energy sword, killing it isntantly. Halsey ripped off jun's dogtags and slowly walked through the smoke in the distance towards the only intact pelican she could spot.
Actually if you read the last few pages of the fall of reach it states that Halsey's pet spartan bodyguard was killed protecting her and that she was the only one to make it back to the base. Which shows how she meets back up with KellY, Fred, and he other live spartan's that where sent to reach, by John, to protect the orbital mac guns power sources.
*posts audio file of darth vader screaming NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO!*he was killed by Al Quidia!