In Trans-Carpathia, Storm Shadow leaps out of the window of a moving train crossing a river. He is detected on scanners by Dr. Mindbender who reports to Cobra Commander as Storm Shadow dives into the river and cuts open a sluice gate to enter the Silent Castle. Storm Shadow thinks he has found the captured Baroness and Billy but suddenly the room all around him turns into giant monstrous faces and hands as Cobra Commander leaps down, carrying giant weapons. The Commander boasts that Dr. Mindbender's Cyber Space Matrix is an environment which is designed to bungle the heightened senses of a ninja. Storm Shadow is unconvinced but is soon disorientated. Cobra Commander is wearing new powered body armour and soon overpowers the ex Cobra ninja.
In the Sierras, Snake-Eyes sits on a rock, so lost in thought that he doesn't notice a rattle snake approaching until Scarlett shoots it dead with her crossbow. She realises he knows Storm Shadow is in trouble and accepts that he must do what he must and go. In the Silent Castle Storm Shadow comes to strapped into the newest version of the Brainwave Scanner, together with Billy and the Baroness. Cobra Commander explains it can totally change a person's outlook and Dr. Mindbender activates the device. Slice and Dice are wondering if they are being made redundant by Mindbender's modifications to make the castle ninja proof and boast that Snake-Eyes will still get through so the Commander orders Dr. Mindbender to activate the matrix. The two Cobra ninjas find themselves standing on a tightrope over molten lava and also under attack from winged monsters looking like the Commander. They are soon restored to reality.
Three days later Flint and Lady Jaye drive through Trans-Carpathia, encountering two Cobra Destroyers. They take out one but the other is soon captured by the newly arrived Snake-Eyes. At the W-Lander Camp, Hawk and Stalker brief Snake-Eyes about the new technology in the castle. Snake-Eyes goes to the tent of General Liederkranz and takes many weapons, also removing his mask.
Later the surviving Cobra Destroyer returns to the Silent Castle with Snake-Eyes holding the crew hostage. He takes care of the guards and uses the Destroyer guns to blast into the castle. Inside he attacks the Cobra troops and defeats many of them. Mindbender reminds Cobra Commander that the latter is still wearing the new armour as they seek to lure Snake-Eyes into the matrix. Soon Snake-Eyes enters to confront Cobra Commander. But Snake-Eyes is not disorientated at all and throws a smoke grenade which interferes with the holographic lasers. He then smashes the control panels and shoots at Cobra Commander's armour. He fires a round containing white phosphorous at the armour which ignites on contact, burning out the power circuits. Cobra troops arrive but are soon disposed of. Snake-Eyes turns to deal with Cobra Commander but the latter is doused by Dr. Mindbender. Suddenly Snake-Eyes finds himself face to face with Billy, the Baroness and Storm Shadow - all now brainwashed and loyal to Cobra! Cobra Commander orders them to kill.