Chain of Command is the fifth episode of the Beast Wars TV series.
The Maximals detect an energon crystal under the cairn in the Standing Stones. Rattrap thinks it reeks of 'bait' and Rhinox notes that the energon on this planet isn't natural, as it does not conform to the planet's geology. The Predacons attack, putting an end to the discussion. During the battle, Terrorsaur purposely fires directly on the buried energon crystal, causing it to destabilize. His prize now useless, Megatron orders a retreat while the Maximals head for cover as it builds to overload. But instead of a debilitating energon wave, it sends a signal to the stars, depleting the crystal's energy. With the Predacons gone and the energon reduced to dust, the bewildered Maximals return to base.
Later, an alien probe emerges from transwarp space and enters the atmosphere. The Predacons initially mistake it for a stasis pod, but Rhinox immediately recognizes it as something else. Both sides head to intercept it at the Standing Stones. Optimus and Dinobot confront Megatron and Waspinator, but when they transform and begin to battle, the probe puts out an energy burst that renders them unconscious and causes Primal to vanish into thin air.
A disoriented Dinobot awakens in the Axalon's CR chamber and, seeing three angry Maximals standing over him, momentarily mistakes it for a Maximal Torture Chamber. The probe, as it turned out, somehow dumped Dinobot, Megatron and Waspinator outside of their respective bases. Believing Primal to be destroyed, Dinobot attempts to take command of the Maximals. Rhinox heads off a fight between Dinobot and Rattrap by insisting on a secret ballot, the traditional Maximal method for resolving such problems.
After the vote results in stalemate, with two votes for each contender, Dinobot giddily rebukes the shortcomings of their peaceful solution. He declares that he will break the tie by force and prepares to attack Rattrap. Before the fight can begin, they are contacted by Optimus Primal, who is not dead. Primal's body has been digitally stored, but his consciousness remains active within the probe. Optimus puts Rattrap in charge. Dinobot glares at him.
Megatron, also believing Primal dead, sends Scorponok and Waspinator to the Standing Stones while the other Predacons attack the Axalon. Dinobot fights Megatron one-on-one, ignoring Rattrap's order to disengage and reset the Axalon's failing shield circuitry. Rattrap scrambles and is able to restore the shields at the last moment. The Predacons retreat when Dinobot beats Megatron back, and Dinobot apologizes to Rattrap for not following his orders, affirming himself "dishonored". Dinobot's uncharacteristic deference and respect makes Rattrap uncomfortable, and he brushes it off.
The Maximals head to the Standing Stones with a device Rhinox has built to attempt to extract Optimus from the probe. The Predacons attack them at the Stones, Rhinox unloading his frustrations on Waspinator when his device malfunctions, blasting him to bits with his chaingun. Waspinator shorts out and comes in contact with one of the stones which activates, revealing the entire Standing Stones site is a single device. The probe opens in response, and Primal materializes. The Predacons retreat before his considerable firepower, but the probe dematerializes before the Maximals can decide what to do with it.
Optimus commends Rattrap on his performance as commander, though Rattrap is more than happy to hand the title back. The Maximals are left wondering what the probe's purpose was, and Rhinox ominously observes the aliens have learned they have the ability to reason... and of their destructive capabilities.