Magma starts by unleashing a jet of molten, erm, magma at Spidey, who, of course, avoids it. Joy and the others are trying to escape but the 'faceless' people corner her. Spidey realises he can't concentrate on Magma and the other three so swings off.
Magma then takes Joy, Charla and Seth into some sort of central complex. We find out that Seth, although slow in some senses, is incredibly gifted mathematically. We find out that the reputable Roxxon company is responsible for the underground bunker. We get the Team-Up 110 flashback where Johnathan Darque - head of the energy company - became Magma to fight environmentalists who were protesting.
He joined Roxxon in a top secret project in the Virginia mountains. He abducted Seth because he wants him to work on a project to use satellites as weapons. Just then the guards bring in Peter (who has let himself be arrested). After being locked up, he and Joy escape and break out Charla and Seth too. Pete gets the others out of the caves to safety but goes back as Spidey to get Magma. Unknown to him though, Joy has hung around with the others to see what happens.
During the course of Spidey's battle with Magma, there's a huge explosion as Spidey causes a malfunction in Magma's costume. It all causes some sort of volcanic eruption (not a big one though). Spidey stumbles across Seth (who's gone back to help Pete) and swings him away to safety with Magma and his gang in hot pursuit. Spidey gets Seth back to Joy and Charla and safety but his web snaps and he is left trapped as the whole cave structure collapses.
In the epilogue, we the mountains smouldering while Joy, Charla and Seth get medical attention. Pete is missing - the only indication he was there is a smouldering red and blue costume...