He is an embodiment of death and is one half of the deity Chronos alongside Zen. Zen had locked him away within the bell tower of the alternate Yasogami High, as he chose to ignore his duty for the time being in order to find an answer to Rei's reason for living. However, he would eventually awaken, starting the events that lead both teams of Persona users to this world.
He does not directly appear for most of the game, but his strongest minion, a Shadow known as the Captor Spider has appeared multiple times throughout in the game. At its beginning, Yosuke Hanamura (P4 Route in Yasogami High School) and Fuuka Yamagishi (P3 Route in Tartarus) briefly notices the spider. Then it appeared in You in Wonderland and notes that time has begun to move, The spider appears briefly before the group again at the beginning of Evil Spirit Club, scaring some of them and leading to a stroll event where they realize something is odd about the spider that could appear in the Dark Hour. His goal was to have them awaken his other self and have them reunite to return to their duty, and once that mission was accomplished they would be allowed to return to their own times. However, he had underestimated the persona users and assumed they would willingly abandon people they have come to care for.
In order for his scheme to be complete, he made the Persona users, Rei and Zen remove the guardians deployed in the attractions in order to make them retrieve the items that awaken Zen and Rei's memories. Once this is done, Clockwork God then becomes the leader of the Shadows appearing in the false Yasogami High School upon completing Inaba Pride Exhibit. He bewitched the bell that trapped the Investigation Team in the High School while the Culture Festival is being held, alongside the SEES in the elevator of the Velvet Room leading them to Yasogami High School. A pile of Shadows appeared in front of Rei and forms into the Captor Spider, which captures her inside it and escapes to the top of the Clock Tower, awaiting the party and Zen's arrival. Once the Captor Spider is defeated, the Clockwork God himself emerges from the gears of the clock tower and attacks the party.
Beneath the iron mask is a face identical to Zen's, which covers up his face during the battle. Seeing that his other half has decided to live as a mortal, Clockwork God has decided to erase him for turning his back on his divine purpose and offers to erase the persona users for choosing to oppose him rather than return home. After losing the battle Zen shatters him, showing gratitude that his own end has come as his body falls apart and vanishes.
The Captor Spider is relatively straightforward. Simply attack away at the head until it retreats behind its legs. If it launches a normal attack, it hits 4 random targets amongst the party. Once it retreats and raises its legs, each leg will then take their action individually, either with a normal attack or a -dyne spell.
For the purposes of conserving SP, have party members equip weapons that deal elemental damage to get free Boost status for more devastating area attacks. Agility Bind is still effective the Spider and its legs, so don't neglect them - cutting their accuracy means fewer chances of losing Boost due to getting hit and fewer turns spent healing off the damage. More importantly, because the spider is immune to every status condition other than binds, Agility Bind is the only way to ensure that attacks such as Myriad Arrows strike the spider.
After all 4 legs are destroyed, the Captor Spider falls forward and is helpless for a few turns, allowing the party to freely attack it. After a few turns it will regenerate its legs and retreat behind them. Attacking the spider in such a way that all four of its legs die at the same time is a good way to optimize the party's damage outputs.
Clockwork God can act twice per turn, and has a normal attack that hits the entire party.
The main obstacle in this battle is the skill Gears of Time, as it is an unstoppable countdown that will kill the affected party member. Naturally, on Risky this means the battle must be ended quickly before Gears of Time claims the protagonist. Clockwork God will not cast Gears of Time unless all party members are currently not affected by it, so keeping a single affected party member alive is more efficient than juggling everyone's counts at once. Using revival spells or items can increase the countdown to delay their inevitable death, but each action spent reviving is an action not spent attacking Clockwork God. On Risky, it is the best idea to leave the protagonist with the countdown while everyone else has already died once to be revived later, while keeping his countdown from dropping to 0 and heavily minimizing the use of revival items.
Fight conservatively, as once Clockwork God reaches 50% HP it will use Time Reversal to restore all its health, however it only does this once per battle. This can be skipped if one does enough damage to put it to 25% HP or lower after that monologue, a goal well within the player's reach should he or she successfully panic the boss, but difficult otherwise. Past this threshold, Clockwork God will occasionally spend its entire turn to "concentrate" - this signifies that the party should spend the next turn Defending since it will use Time Stop next turn, allowing it to perform 5 attacks in a row.
Perhaps fittingly, Clockwork God is disproportionately susceptible to paralysis.
"The time has come. The time to fulfill your role. The time to return to your original form. You have forgotten your role. You resisted your duty even after regaining your memory. You have reduced yourself to a mortal. You have reduced yourself to that which is unnecessary. I shall erase myself. I shall erase you, a part of me. I shall return everything in this world to ash. The time has come." (75% HP)
"Players, you have done your part well. Yet, why do you not return from whence you came? The curtain has fallen... Why do those who are destined to perish defy me? You are humans; your frail kind requires my protection. But if it is your wish, then I shall erase you as well." (50% HP)
"I am Chronos... I was born from man, and accompany man on his journey... You wander an ephemeral dream... Your transience affords you uncompromising power... What is your life...? What is your death...?" (25% HP)
"Hugh!" (When attacking)
"Ha!" (When attacking or using Vorpal Sword)
"Tch!" (When attacking or using Vorpal Sword)
"The time has come..." (Using Gear of Time or casting a spell)
"The time to reverse time..." (Using Time Stop)
"This is enough time..." (Ending Time Stop)
"Prepare to meet thy fate..." (Using Time Warp)
"The time to return to whence you came..." (Casting a spell)
"Take this..." (Casting a spell)
"Ugh!" (When attacked)
"Ngh!" (When attacked)
"..." (When attacked)
"This couldn't... how could it be...?" (Upon being defeated)
The Captor Spider's Japanese name might refer to how Rei was trapped inside it.
The Clockwork God's motives mirror Enlil's motives in the game's sequel. While the Clockwork God wants Zen to move forward and complete his mission, Enlil stagnates the people that she is supposed to protect in her Cinemas and prevents them from moving forward on their lives.
Unlike most MegaTen antagonists, the Clockwork God appears to have neither ill-intent nor is he misguided in his actions; He is merely attacking the party out of self-defense and his motive is to keep worldly order.