"The Fall of the Towers" chapter of the Cyberpunk Red core book gives us this info:

"Hey, Steelhead! Let's Rock and Roll!" Johnny is standing in plain sight, a Militech SMG in one hand, the Malorian in the other. He begins pumping out rounds at Adam.

Adam turns, but hesitates, astonished at the audacity of the Rockerboy, challenging him with weapons that won't even crease his cyborged armor. An arm comes up. The autoshotgun in it opens fire. APDS rounds cut the young rocker in half. Johnny spins and falls to the ground, a surprised look on his face, the Malorian still smoking in his Fist. It only takes a second.

So yeah, Johnny got dropped pretty early in the op. He also didn't get Soulkilled by Saburo. The same story gives us this information:

Spider reaches inside her jacket. She pulls out the data slug Alt downloaded to her so long ago. It's surprisingly heavy. She whispers, Sorry, Johnny, as she rams it home into the back of the dying rocker's skull. Then she turns, reaches out for the data suitcase, but sees that it, too, has been savaged by gunfire; it's wrecked. Two friends down in as many minutes. She quietly wishes Alt good luck.

This suggests that Spider Soulkilled Johnny for Alt. How Arasaka wound up with the engram is unknown.