On May 10, 1989, and his partner were driving their vehicle alongside the railroad tracks in an area of the El Paso Sector known as the "slag pits." They were preparing to check an outbound Southern Pacific freight train. There were three separate sets of tracks in the area, two used mainly for outbound trains and running parallel to each other and the other used mainly for incoming trains. The thirds set curved inward toward the other tracks, forming a rough triangle. Inside the triangle were numerous piles of slag, 6 to 15 feet high.

The agents were driving east between the slag piles and outbound tracks. A train was coming toward them on these tracks. Once clear of the slag piles, Agent Magdaleno tried to execute a 180-degree turn. The wheels of the vehicle began to slide in the soft slag. The vehicle would not respond to the steering wheel; instead, it plowed forward, alongside the incoming tracks. The agents did not see the incoming train because of the slag piles and the curve of the track until it was about 75 yards from the vehicle. Agent Magdaleno put the vehicle into reverse in an attempt to get out of the train's way. However, the train struck the vehicle on the passenger side and threw the rear of the vehicle toward the track. It was again struck by the still-moving train.

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On the initial impact, Agent Magdaleno's partner was thrown out of the vehicle away from the train. The second impact threw Agent Magdaleno out of the vehicle, and it came to rest on top of him. He was pinned under the wreckage for 45 minutes. When freed, he was taken to R.E. Thomason General Hospital, where surgery was performed. He was paralyzed from the neck down, requiring ventilator assistance. He died from his injuries on May 10, 1995.

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Agent Magdaleno was a graduate of the 139th session of the Border Patrol Academy and was assigned to the El Paso Station at the time of his death.