appearances and encounters
You first encounter Cyrus at Lake Verity, which is just north of the player's hometown of Twinleaf. You and your rival overhear him give an ominous speech to the "Legendary Pokemon of the lake bed", where he declares that all of space and time will be his, after which he passes by the two of you to leave the wooded area, where he asks that you step out of his way. Your next encounter with this weirdo is a similar situation in Eterna City. Where he's once again giving a strange speech about space and time, this time to a statue instead of a lake. He speaks for a moment about how Sinnoh's myths need investigation, and once again politely asks you to move out of his way when he leaves.
Mt. Coronet is the next place you run into him, and it's where you get to have a one-on-one conversation with him, instead of just eavesdropping on him talking to inanimate objects. Cyrus walks up to the player seemingly out of nowhere, and gives no introduction before spiraling into a rant about how the human spirit is incomplete and that it only causes strife and pain for humans, then walks away without another word. Even if it's a bizarre encounter, it's the player's first real glimpse into his ideals & views on the world.
The next time you speak with Cyrus is much later into the game, at the Celestic Ruins, after you defeat a galactic grunt standing outside that was threatening to blow up said ruins. He interrupts your talk with an elder of the village and proceeds to interrogate her about what exactly the mural on the back of the cave means, and after she won't give up the information. He goes off once again about how the human spirit is weak and incomplete and challenges you to a battle for opposing him. After you defeat him he doesn't seem angry, he actually seems quite impressed with you. He then says that he has all the information he needs, says something ominous and foreboding, then leaves.
At the Team Galactic HQ in Veilstone city is where you meet him next, first watching from the shadows as he gives a speech to the grunts about the grand finale of his plan to remake the world. Then after following you into his office where he seems to be expecting you. Cyrus informs you that what he had told his grunts and commanders was a lie, that the new world he was planning on creating was not for all of Team Galactic, but solely for him to be the god of, where he alone can shape it into his ideal universe, devoid of the incomplete human spirit. He realizes that you're here to free the three lake guardians, and at first, seems to be fine with this, but then becomes intrigued on why exactly you care about freeing these Pokemon and challenges you to another battle to try and prove to you that your incomplete spirit is your downfall, for leading you to put yourself in jeopardy to save the lake guardians.
You defeat him, of course. And just like in the Celestic ruins, he doesn't seem upset at you, more so disappointed that he couldn't make you understand his point of view. Then he does something completely out of left field and hands the player a master ball as a "reward". Which is something I can't even begin to get into right here; so if you want to hear more about this specific moment, see my theories page.
Moving on, you then need to immediately head up to Spear Pillar, which is at the very top of Mt. Coronet, where you find Cyrus and his two commanders at the center of the ruins with the Red Chain, ready to summon the two legendary pokemon, Dialga and Palkia, which he will use the power of to destroy this world and bring everything back to zero. Once they are summoned and under the control of the red chain, the three lake guardians fly up to the top of Mt. Coronet, but it's no use. The three of them combined aren't quite strong enough to stop the two deities. He turns to the player and tells you that despite all the trouble that you've caused him, he forgives you, as it doesn't matter now what happens. But right as he's about to put his final plan into action, an unseen force causes the sky to darken, and the lake guardians to spin out of control in the air above him. Just as Cyrus states that he can feel an angry presence, a massive black beast claws out of a hole in the ground in front of him, seemingly appearing from nowhere at all. Cyrus seems to have expected the creature, as he doesn't seem alarmed at first, simply trying to tell the beast that his plans will move forward regardless, only starting to step back in fear when it spreads its massive wings and rears to attack, and then lunges at Cyrus, both him and the creature disappearing into the ground where a portal is left in its wake.
After the dust settles, Cynthia makes her way to Spear Pillar just a second too late and tells the player that they have to follow Cyrus into this other world to stop him for good. [I'm so over this section rn]