This page of the Biomutant guide contains a detailed walkthrough of The Ark story quest.
Out-of-Date has figured out how the Ark works. If the worst scenario happens, there may still be a way for some to escape. Besides the Sifu of the allied tribe, Out-of-Date and you, there is still room left for four passengers. It is up to you to decide who gets one of these seats.
Decide who'll go with the Ark
You can offer a place on the Ark to people you've already met or save it for anyone you'll meet later on. This option is unlocked when you have completed all quests for a particular NPC. Think carefully before inviting or declining a seat on the Ark, as you will not be able to undo that decision.
You can invite up to 4 people to the Ark, but you are not obligated to use all the seats.
Can NPCs refuse a seat on the Ark?
Some NPCs you meet on your way in Biomutant may refuse the offered place on the Ark, which may be related to your choices or aura, for example.