If you are playing a Linked Game of Oracle of Ages (a game that you started by inputting a Secret to Labrynna password obtained by beating Oracle of Seasons), then the Room of Rites is where you are sent after defeating Veran. There you will face the true final bosses of Oracle of Ages.
Eye of Deceit
Go north from the Room of Rites entrance. Wait for the statues' eyes to stop spinning, then go in the direction that none of the statues are looking in. You will go through about seven rooms this way.
Eventually you reach a room where the statues have no eyes. Just go north here. Go up to Zelda.
Koume and Kotake
To defeat these two, knock the fireballs at the blue one (Kotake) and knock the ice balls at the red one (Koume). After you have hit them enough times, they merge to become Twinrova.
The merged Twinrova will switch between three forms: fire, ice, and both.
While Twinrova is in fire form, the floor will have lava pits. You have to hit Twinrova with your sword to damage her, but hitting her knocks you back, which puts you at risk of falling in the lava. If you have the Steadfast Ring, use it to prevent getting knocked back.
Use the Snowshoe Ring if you have it to prevent sliding on the ice. Hit Twinrova with your sword. You can hit the ice balls with your sword to prevent them from hitting you.
When Twinrova is a mix of fire and ice, and if the floor has lava pits, hit Twinrova with Mystery Seeds, and if the floor is covered in ice, hit Twinrova with Ember Seeds.
After Twinrova is defeated, Ganon attacks. If you have the Noble Sword, you have to use spin attacks to damage him. With the Master Sword, you can just hit him with no need to spin attack. Biggoron's Sword doesn't work on Ganon. Sometimes the background will turn blue. This means that the controls are reversed, so you have to press up to go down, press left to go right, and so on.
Ganon warps to random spots on screen. He swipes with his Trident, and sometimes uses the trident to create fireballs. Sometimes he shoots medium fireballs at you, and sometimes he creates small fireballs around himself. At times Ganon pounds the ground. Be sure to jump when he does that to avoid getting paralyzed by the shockwave, then get ready to run out of the way of the large fireball that he shoots afterward.
After Ganon is defeated, go to the bottom-right of the room and go up the stairs, then check on Zelda.
Congratulations! You defeated Ganon! Enjoy the full Oracle of Ages ending!
Afterward, be sure to make a note of the Hero's Secret. If you want to experience the non-Linked version of Ages (rather than the Linked version that you just finished), use the Hero's Secret to start a new game of Ages. Rather than starting from scratch, you'll start with four hearts instead of three, you'll have the Victory Ring in your list, and you can use the Ring Secret from any game to bring all of your rings to the Hero's game. This makes it easier to collect all 64 rings.