Timeline 1

Timeline 1, commonly referred to as the main timeline, is the main timeline where the events of Zero and Zero: Origins take place. There is one person who interfered with this timeline: Dr. Murphy, interfered with the timeline when he came back in time to find and stop Present Xeno from causing chaos that would lead to a horrible future.

When Dr. Murphy went back in time, it disrupted and altered Timeline 1, making an "Altered Timeline", or "Altered Timeline 1", overwriting events portrayed in Zero: Origins. Zero takes place in this Altered Timeline. However, it is still Timeline 1, just like Zero: Origins.

Events
Timeline 1, as noted above, is the main timeline where everything takes place. It is similar to Timeline 2, however a major difference present in Timeline 2 is that Zero was created as an android instead of an AI, Aero was never built, and Zero and Xeno have been archenemies for quite some time. Timeline 2 Zero's fate was never revealed. When Dr. Murphy went back in time, he had the intention to change history, altering this timeline. However, simply going back in time had disrupted the timeline.

Original Timeline

 * Dr. Murphy is born in an unspecified year.
 * Dr. Cyanide is born five years later.
 * Dr. Murphy starts creating prototypes for robots with Dr. Cyanide at the age of 20.
 * Dr. Cyanide turns on Dr. Murphy and the two become enemies after ten years.
 * Xander Ziegler is created by an unknown scientist on an unknown date.
 * Drake Edwin is born on an unspecified year.
 * Dr. Murphy creates Black, but he later escapes and runs away
 * Julian Tatsuki is born on an unspecified year.
 * Millie is born on an unspecified year.
 * Future Xeno is created by another unknown scientist and put on sleep mode for 31 years.
 * Cooper is born one year after Future Xeno is put into sleep mode.
 * Summer is born one year later.
 * Sonic, Diamond Man, and Ring-8 are created by three unknown scientists.
 * 25 years later, Xeno arrives from Timeline 2 and goes into sleep mode for five years.
 * Five years later, Xeno wakes up, captures Future Xeno, and starts to cause chaos.
 * Dr. Murphy creates the AI Zero as his assistant.
 * Dr. Cyanide allies with Xeno one year later and creates his army of robots
 * Dr. Murphy creates Aero to stop Dr. Cyanide and his army of robots, as well as Xeno and their doomsday device.
 * Aero stops Dr. Cyanide's plans and confronts Xeno, shutting down the doomsday device but killed when Xeno bombs the area.
 * Dr. Murphy goes back in time with Zero, and when they arrive, it has been twenty years after Cooper's birth.

Altered Timeline

 * Three years later, Dr. Murphy finishes giving Zero a body, his ultimate creation.
 * Events portrayed in Zero take place.
 * Zero marries Summer five years after the end of Zero.

Major Differences
Events from the Original Timeline still happen in the Altered Timeline. 20 years after Cooper's birth, however, is where the events of the Altered Timeline begin to take place, overwriting the events of the Original Timeline. Generally everything in Zero is different from the Original Timeline.
 * Xeno's arrival from Timeline 2 still happened. However, Xeno returns from the future at the same time as Dr. Murphy, and goes into sleep mode for five years. After waking up, Xeno starts his chaos, knowing that his past self is in sleep mode.
 * Villains such as Kane, Neo, Julian, Sonic, Multiplex, Frozin, XYZ, and many others appear in the Altered Timeline, but are civilized people in the Original Timeline.
 * Humankind and civilizations are more advanced than they were in the Original Timeline.
 * Aero does not exist in the Altered Timeline, as the Altered Timeline overwrites events in the Original Timeline, events portrayed in Zero: Origins.
 * Dr. Cyanide does not build his army of robots and the doomsday device, however this is because he is killed by Xeno in the Altered Timeline.