Magnetron is played out across a number of different space stations. Demon droids have taken control of eight armed stations in orbit around the planet Quartech. The player controlls a Meknotech droid called KLP2, who was beamed aboard the first station (Magnetron) in an attempt to shut down each of its four reactors. This process has to be repeated for each station in turn.
The stability of each reactor is dependent on the combined charge of its fuel rods (+) and its inhibitors (-). By switching the charges around, KLP2 either shuts down or destroys each reactor. By steering KLP2 over a terminal and pressing fire, the player sees KLP2's current attributes, the state of the reactors and so on.
Every satellite is occupied by demon droids. KLP2 has limited weaponry, but he can shoot at demon droids and they can shoot back. Alternatively, KLP2 can 'grapple' with each droid in a brave attempt to overcome it and assimilate some of its components, thus upgrading KLP2 in the process. To do this, the player presses fire and enters 'grapple' mode (indicated on the main game control panel). He then collides with a demon droid to enter the grappling phase. A new screen pops up where the grapple is decided against the clock. The player is faced by a 3x3 grid of nine icons, with three of each type. The idea is to rapidly move the icons so that the same icons line up together on the grid (three rows of three icon types) before the timer runs out.
Each time the player manages to upgrade, KLP2 effectively adds an extra life to his attributes. If he loses power, then he reverts to his previous chassis (at the location within the station where the previous grapple had been won) and continues on his mission. Once all the lives are used up, it's game over. Arrow tiles on the floor force KLP2 into that particular direction, and moving in the opposite direction over those tiles puts a strain on KLP2's power source.
The demon droids all have designations, so the player can see if the droid is worth grappling with or not. When KLP2 upgrades, his security level can increase and more information (about the components - drive, power source, weapon and finally device) becomes available via the terminals dotted around each station.
Setting a reactor to shut down or overload involves locating the reactor, moving over it and pressing fire. The player then has to add or subtract values from the fuel rods and inhibitors until its status changes from 'stable' to 'shut down' or 'overload'. Each terminal shows the status of the four reactors on the station.
Magnetron uses isometric 3D landscapes of ramps and terminals. The player moves KLP2 across and up or down the ramps to enter the next screen. It looks quite similar to it's predecessor "Quazatron" (written by the same programmer and published by Hewson a few years previously), and some of the gameplay is very reminiscent of that game.