Many issues can require that a player be able to leave the table (often unannounced, or with an irregular frequency). 

If the reason for leaving the table is due to a need for certain facilities, ensure that those facilities are accessible.  If the player needs to move to an area that supports their desire for feeling safe (a safe space) try to determine the needs of that environment in advance, and make that environment available.  This could be something as simple as putting a comfortable chair in another room.  If the player is a child, or has a support care giver, the exact requirements may be best determined in a initial Pre-Session Communication meeting.

If leaving the table is frequent, or persistent, and other players are affected by the absence, you can attempt to roll the disappearances into the narrative, so long as the accommodated player allows for it.  

Ex. “As you’re fighting Agent Orangutan, Tom notices scientific personnel outside of the room trying to flee for safety. With a nod to his compatriots, he valiantly leaps through the door to ensure their safety.”
Reduce difficulty for the time within that campaign while the player is gone.  Additionally if the player is amenable to the idea, you could set their character into a somewhat autopilot mode, where other designated players or the GM their self takes control over the heroes actions.

If the player is the sole member of the team, and no other players are impacted, you can feel free to simply pause the game, and utilize the time toward future planning.