When Zion's attack became imminent, the Council inquired of the fate of Morpheus and his ship, the Nebuchadnezzar.The Logos and the hovercraft Vigilant volunteered to search for the Nebuchadnezzar.
When they met, the crew of the Vigilant volunteered to help Morpheus assist the One to enter the Source. Their task was to disable a backup generator of the local nuclear plant.
Everything went according to plan, and the Vigilant crew immediately began disabling the backup systems after Niobe destroyed the power plant. However, in the Real World, things went horribly wrong.
Axel was with Jax at the operator's console, when the ship's Proximity Alert went off, alerting the two to the presence of nearby Sentinels. Axel ran toward the cockpit to confirm the presence of the Sentinels. He went back to warn Jax but the catwalk collapsed on his way, making him fall to his death while one of the catwalk support columns impaled Jax.
Meanwhile, one of the Sentinels proceeded to fire a Tow Bomb at the ship. The bomb hit the Vigilant and exploded, killing everyone on board. Inside the Matrix, the avatars of Soren, Binary and Vector collapsed, their real world bodies killed during the destruction of the Vigilant.
Trinity and Link heard the explosion from the Vigilant's destruction, which led to the chain of events leading up to Trinity's death and resurrection.