Myst V: End of Ages is an adventure game taking place in the first person. Players travel across several worlds known as "Ages", solving puzzles and gathering story clues by reading books or observing the environment. End of Ages offers players three navigation modes to explore. The first, "Classic mode", uses the same controls used in Myst and Riven; Ages are divided into locations of interest, or nodes, and the player's view is fixed at every node. Players advance to other nodes by clicking on portions of the screen. The "Classic Plus" mode uses the control scheme of Myst III: Exile and Myst IV: Revelation; movement is still node-based but players can rotate their view 360 degrees in any direction. The final navigation mode, known as "Free Look" or "Advanced" mode, allows players to navigate and observe the Ages freely like Uru: Ages Beyond Myst. The WASD keyboard keys are used for walking forward, backward, and sideways, while the mouse changes the player's point of view.
A new game mechanic to the series is the use of a slate found on all the Ages. These slates can be carved using the mouse to create shapes and symbols. The use of the slate is necessary to communicate with a shadowy race of creatures known as the Bahro. The Bahro understand certain symbols drawn on the slate and will respond to them; the creatures also retrieve the slate and return it to its original space if the player drops it. Slate symbols can cause environmental changes such as rain or increased wind, which may be necessary for solving puzzles. The slate cannot be carried everywhere due to its size. For example, the player will have to leave the slate behind if he or she wants to climb a ladder.
End of Ages has several features designed to help players complete puzzles. To recall clues or important items, players can use a camera feature to take screenshots, which are then placed in a journal the player can access at any time. Player interactions with other characters are similarly recalled via another journal; everything a character tells the player is stored and can be viewed at any time. Journal pages are narrated by the voice of the character, and missing pages of the journal appear translucent in menus.
End of Ages takes place in the present day, sometime after the events of Uru: Ages Beyond Myst, and begins as the player responds to a letter from Atrus. Atrus is a writer of special volumes called linking books, which serve as portals or links to worlds known as Ages. A linking book to the Age of Myst, the setting of the original game, lies sealed in the ruins of the ancient D'ni civilization. The D'ni had the ability to craft linking books, but their society crumbled from within; Atrus and his family have been trying to restore the D'ni people and created an Age for the survivors to live on, known as Releeshahn (introduced in Exile). Atrus by this period is an old man, mourning the deaths of his sons Sirrus and Achenar in Revelation, and the death of his wife Catherine in the period after. In his letter, Atrus expresses concern that his daughter, Yeesha, may be lost as well.
The player starts in Atrus' old study on K'veer, an island near the ruins of the main D'ni city; in the antechamber outside the study, there is a strange tablet locked in place on an altar. Yeesha links in and explains that legends state that in order to fully restore D'ni, someone known as the Grower must utilize the tablet. The artifact has the ability to fully control a mysterious enslaved race known as the Bahro. As Yeesha made the wrong decision upon unlocking the tablet, she can no longer use it; Yeesha instead charges the player with uncovering the tablet's power. After leaving Yeesha, the player meets a man named Esher near "the Great Shaft", connecting D'ni to the surface (as detailed in Myst: The Book of Ti'ana). Esher is a survivor of the fall of D'ni and tells the player that Yeesha cannot be trusted, warning the player not to give her the Tablet. Throughout the Great Shaft, the player collects twelve fragments of Yeesha's journal. The writings appear to confirm Esher's warnings, as the narration seemingly indicates that Yeesha has descended into madness, believing herself to be the Grower.
At the urging of both Yeesha and Esher, the player travels across four Ages, collecting four slates that unlock the tablet's power. Esher occasionally appears in the Ages to offer his counsel, or reveal the histories of his people and the worlds the player explores. Once all four slates are collected, Esher requests that the player bring the tablet to him in the now-unlocked Age of Myst. The player is then returned to K'veer, where they have four possible choices. Travelling to Myst without the tablet will cause Esher to angrily abandon the player with no way out. If Esher is given the tablet, he will explain he wishes to use the tablet for domination, and will also leave the player trapped. If the player gives the tablet to Yeesha, the tablet simply slips through her hands and disappears into the ground; she walks away, disappointed, leaving the player trapped in D'ni. The only good ending involves giving the Bahro the tablet, ending their enslavement. Arriving at Releeshahn, the new home Age of the D'ni, Yeesha and Atrus thank the player and speak of a new chapter for the D'ni people; Esher is handed over to the Bahro to be punished for his crimes. The game ends on a visit to Releeshahn.