The player begins the game in one of three ships with basic equipment, a few credits (one of the two in-game currencies), and a near-empty cargo bay.

The player collects money and items by several means, such as trading, looting the remains of destroyed ships or stations, escorting freighters, or agreeing to medical experiments.

However, if the shield is depleted then the player's individual armor segments are damaged depending on the angle of incoming attacks.

Transcendence is installed with one storyline (known as an adventure), The Stars of the Pilgrim which is a part of the "Domina and Oracus" trilogy.

Within the galaxy are stargates, devices used for faster-than-light interstellar travel, left behind by alien races.

In 2363, years before the game takes place, humans made contact with the Iocrym, who are members of the ancient races.

The player, referred to as a pilgrim, leaves their home in a station in the Eridani star system and visits a monastery, where they are given training for their journey by the Sisters of Domina.

Fighting through Iocrym forces, the pilgrim reactivates the outer stargate, allowing them to continue their journey.

It features an XML format with scripting in TransLISP, a custom Lisp dialect designed for the game.

It allows players to rewrite and add in-game objects, or even Adventures that create brand-new settings and game stories.