Uldren Sov was indeed imprisoned there.
Following the events of The Taken King, everyone thought both Uldren and Mara Sov were dead. However, Uldren somehow survived, and ended up shipwrecked on Mars.
The sound of her voice ripped him from sleep. He jumped up; his ship was still contained in its protective sphere. He tried to retract the shield, but it was locked to its initiation time. He couldn’t remember activating it. Then he remembered the battle. That blast.
(...)
He climbed out and saw the damage to his ship, and the truths of the armada's devastation sunk in.
He turned in despair to find hundreds of his Crow drones, deployed on Mars long ago, circling his ship, waiting.
“Welcome back, Master.” The one closest to him spoke first, and the others followed, a wave of salutations echoed throughout the dry sea.
And with that hope returned.
“Begin repairs on the ship immediately. Something has gone missing and you will help me find it.”
There are hints he might have an affliction of some kind, after he survived the blast at the Battle of Saturn.
There is something in his eye. He blinks and blinks, trying to rub it away, and as he does, he struggles to hear her, to sense that prickle of starlight under his skin. She will tell him he is on the right path. She will tell him she's still alive.
He feels nothing.
Uldren spent some time with his allies from the House of Kings. At some point in time, he confronts Illyn, as described in the lore entry Free | Part I:
"Admit it! Admit that you trapped my sister in the Dreaming City!"
(...)
That evening, he surrenders himself to the Reef.
In the next entry, Free | Part II;
They take him to a discreet landing dock on one of the lower levels of the Prison of Elders. When his containment unit hisses open, the glow and the mist silhouette an Exo with glowing blue eyes and a woman with her weapon drawn. Petra herself.
Petra Venj makes sure that only those three - Cayde-6, Petra, and Variks, know that Uldren Sov is in the Prison of Elders:
"I know. It's… Something's wrong with him, Variks. He's… mad. Lock him down—lock down the entire cellblock. No one in but you or me. Speak of this to no one. As far as the system is concerned, Uldren Sov died over Saturn."
Variks, who is the warden of The Prison of Elders, does not know where his loyalty truly lies. After a while, he shows that his loyalty lies with Uldren, opens all cells in the prison, and escapes through the same secret passage that they used to smuggle Uldren through undetected while the prison is in chaos.
Uldren escapes, and continues his campaign to free his sister, which he believes is still alive.
