Alpha Line

The Alpha Line is the timeline that was created after Obsidian Synis had kidnapped Topaz and Cerise Rosso, Cyan Oak, Jade Sakaki, Rubin and Sapphira Senri, Esmeralda Emerarudo, Plato Berlitz-Palmer, Jasper Daiyamondo, and Grey Kuro, the children of the fifteen Pokedex Holders. The timeline that revolve around what would have happened if Synis had never kidnapped the children of the Dex Holders. The events of the Alpha Line occur in the distant future, starting in the year 4998.

The Forever Trilogy
In the Alpha Line, the government made it illegal to associate with Pokemon in any way. However, the Resistance was started around 4900 to fight against the government and their anti-Pokemon laws. In 5000, Synis declared war on the rebels, by bombing Little Root Town.

By 5001, Synis had been defeated and the Resistance worked to reunite humans and Pokemon.

Evermore
Because of Synis's tampering of time, time has been slowly unraveling. By 5020 in the Alpha Line and 2053 in the Beta Line, the two timelines have combined.