The Paradox Engine only appears in the Allied Act Two campaign and can be considered an epic unit.
Seemingly the culmination of the Allies' Paradox Project, in direct combat the Paradox Engine is armed with an array of prism refractors and missile batteries that can fire on both ground and air targets. It is also the most durable airborne vessel throughout the war, making it a formidable opponent - though it is still vulnerable to concentrated anti-air fire, as seen during its escape through the Isles of Sicily where the Epsilon Gehenna Platforms must be eliminated to allow the Paradox Engine safe passage.
If spawned outside of its mission appearances (such as the FinalOmega map editor), its weapons are disabled by default to prevent cheaters from exploiting the unit in online matches.
The Paradox Engine seems to have been developed jointly as part of the Paradox Project by SteinsTech and KI scientists after the Soviet invasion of Britain is repulsed. Its initial goal is to invade Moscow and put an end to the Soviets and their occupation of Europe, although this ended up being a moot point.
By the time the Yuri and his Epsilon Army emerge as a new threat, the Engine, which is still at its developmental stages, was forced to be prematurely launched when Epsilon forces attacked London. During its escape, the Engine activates the Time Freeze, which results in the destruction of the invading Epsilon forces, including their prized Aerial Fortress Irkalla.
As the Paradox Engine heads to a safe place with the survivors of the London attack, they became aware that Epsilon has set an ambush on the Isles of Scilly. Fortunately, with the help of the Allied Commander and the newly formed Chrono Legion, the ambush is thwarted and the Engine can safely proceed.
Unfortunately, just as the Paradox Engine is about to reach the Canary Islands, its power is running low thanks to its earlier launch than intended and the continuous use of its Time Freeze, forcing the Allies to recharge the Engine's power by "borrowing" Epsilon Bio Reactors in Tenerife. It takes a while before the Engine is back at full power again, at which it once again uses its powers to stop time, allowing the Allied forces to destroy the Epsilon forces in the blink of an eye.
The Paradox Engine later sends a task force via chronoshift to the US Virgin Islands, when the local Pacific Front garrison requests the Commander's help in defending their new Weather Control Device from Epsilon and mind-controlled Russian forces. When Yuri builds a new Psychic Amplifier with the purpose of taking over the Weather Controller, the Engine's Chronosphere is used to send Tanya and Norio to raid the Amplifier and destroy it. It later chronoshifts a large Allied army to Cape Town, South Africa to destroy the Epsilon naval base and communication junction, in the process locating Yuri's headquarters in Antarctica. Unfortunately, just as the Paradox Engine arrives at Cape Town, Epsilon forces manage to sabotage the Paradox Engine's backup battery, forcing the Allies to recharge at Cape Town before striking at Antarctica.
The Paradox Engine spearheads the Allied assault on Antarctica, making short work of the Epsilon defences in the Weddell Sea and the Pensacola Mountains, heading towards the South Pole and easily resisting all Epsilon attempts to shoot it down. Despite the loss of its backup battery, which means that the Engine has to be powered down completely to be recharged, it continues to use the Time Freeze to a fairly frequent degree.
- The Paradox Engine first appears at the end of Godsend. As the Epsilon task force rampage through London and approach the SteinsTech Hangar, headquarters of the Paradox Project, the Paradox Engine emerges and uses its Time Freeze ability to slaughter every Epsilon soldier before making its escape.
- The Paradox Engine is en route to the Isles of Scilly, Cornwall at the beginning of Bottleneck. The first part of the mission involves using a group of Chrono Legionnaires to erase the Epsilon anti-air weaponry that might pose a threat to the Paradox Engine (most importantly Gehenna Platforms, which will eventually destroy the Engine if even one is left alive). In the second part of the mission, the Paradox Engine arrives and must be escorted safely through the Epsilon lines, after which it will use the Time Freeze and allow the remaining Allied forces to clear the Epsilon presence in the isles. The Paradox Engine is not directly controllable by the player in this mission, but rather follows its designated path and uses its weapons automatically.
- The Paradox Engine does not appear physically in Hysteria and Relentless, but will only provide chrono reinforcements during the early part of the mission (see Chronoshift).
- In Relentless, after the MCV arrives and the chrono reinforcements are disabled, the Paradox Engine will grant access to the Chronosphere's Chronoshift superweapon. The Paradox Engine itself arrives at the very end of the mission, after the Epsilon forces are destroyed.
- At the beginning of Insomnia, the Paradox Engine uses the Time Freeze just before the initial landing of the Allied forces on Antarctica; after a few minutes, it will physically arrive with a wing of elite Thor Gunships, then falls under control of the player, starting at elite rank. In addition to the Chronoshift like in Relentless, in this mission the Time Freeze can be manually activated by the player as a support power. The Paradox Engine must not be destroyed during the course of the mission, and the player will be notified if its health drops under 50% or 33%. Once the Epsilon forces are destroyed, it will move south, towards the main Epsilon Headquarters.
- In Unthinkable, after enough time passes, the Paradox Engine will appear. Yuri will instruct the Proselyte to focus all firepower on it, but this attempt is futile as the Engine activates the Time Freeze and destroys the Epsilon forces once either it is on low health (red, lower than 25%) or it gets close to the bottom side of the map.
- The Paradox Engine's unit ID in the game files, [STARDUST], is possibly a reference to JoJo's Bizarre Adventure: Stardust Crusaders, specifically, to the villain (and later main protagonist's) ability to stop time with their Stands.