Mon Mothma can be seen leading the Rebel Alliance on Yavin IV in Rogue One: A Star Wars Story, but she's no longer there just a few days later during the events of Star Wars: Episode IV - A New Hope. The Star Wars prequel trilogy details how Darth Sidious, known universally by his public persona of Supreme Chancellor Sheev Palpatine, was able to use the Clone Wars and the Separatist threat to consolidate power and transition the millennia-old Galactic Republic into the totalitarian Galactic Empire. The new regime held a tight grip on the galaxy but was met with a measure of resistance almost immediately, started in part by Mon Mothma.
Although her appearance in Star Wars: Episode III - Revenge of the Sith was excised, Mon Mothma was a respected senator in the days of the Galactic Republic. Along with a few other concerned politicians, including Padmé Amidala and Bail Organa, Mothma was an early voice of dissent against the expanded powers that Supreme Chancellor Palpatine was assuming in the midst of the Clone Wars.
As shown in Rogue One, Mon Mothma was heavily involved in the Rebel chain of command in the lead-up to the theft of the Death Star plans. However, she is not seen at all during the Battle of Yavin in Star Wars: Episode IV - A New Hope. Her whereabouts at that time are, however, explored in one of the short stories in the From a Certain Point of View collection. Before the arrival of the series' protagonists on Yavin IV, Mon Mothma is sent off-planet as a contingency plan, so that the highest Rebellion leadership would live on if the assault on the Death Star failed. Originally bound for anonymity in the Outer Rim, Mothma decides en route to go instead to Coruscant, where she might face the consequences of failure without endangering further lives. Thankfully, because Luke Skywalker manages to destroy the battle station, Mothma does not have to confront this last resort and is able to return to the Rebellion, which she is later seen leading in Return of the Jedi.
Bail Organa co-founded the Alliance to Restore the Republic with Mon Mothma and led it alongside her in its early years. As such, Organa's death in the destruction of Alderaan only a short time before the Battle of Yavin threw the leadership of the Rebellion into flux and Mothma, already a central figure in the movement, would likely have had a wealth of new responsibilities as the sole leader of the Rebels. Additionally, given the special significance of the recent Battle of Scarif to the Galactic Civil War as a whole, the preservation of the Rebellion was more essential at that time than ever. Both of these factors likely contributed to the extreme caution of the contingency plan.
The frequent skirmishes and space battles of the original Star Wars trilogy tend to obscure the fact somewhat, but the Alliance to Restore the Republic was more than a loose coalition of fighters; it was a political movement that involved leadership and representation. Mon Mothma adhered fervently to the Alliance's core ideals even after the war, when she became the first Chancellor of the New Republic and pushed for large-scale demilitarization. In light of this, it befits Mothma's uniquely dedicated pacifism that she does not directly take part in one of the most famous battles of the Galactic Civil War, knowing that someone in her position could better serve the Rebellion in a different way.