In the Paradox universe, this Marcellus has been heavily modified with Mecha-based equipment. Also, unlike the original trilogy, he is still very much alive and is the person who has diverted most from the correct history. All because he is trying to stop the spread of chaos.
Marcellus is mentioned numerous times throughout the trilogy (I can't include every time he is mentioned, so I'll just put in the significant bits. If I've missed anything important, let me know, or feel free to add it in yourself.)
At the start of the game, reading Luka's diary and talking to the village chief reveals that Marcellus had left Luka at a very young age, but the exact age of Luka when Marcellus left is not disclosed. Before Luka was born, Marcellus and a group of companions set out to travel the world after the events of the Great Disaster, helping those in need. Marcellus did return to the village eventually, and he met his future wife, Lucifina. The exact details of how they met aren't known.
Shortly after they got together, Luka was born, but after that, Marcellus set out to defend the people he loved, Luka, and Lucifina. He left the village, explaining to the villagers that he had to drive the darkness covering the world out, and hasn't been seen again since. Lucifina knew why he had to go, but she never told anyone, and she took that secret to the grave.
Luka finds more information on his father in Rostrum Alt. Once the party enters the village, the group are greeted by a man who mistakes Luka for Marcellus. He is glad that "Marcellus" enjoys visiting the village so much, but is confused how he manages to look so different each time he does. This is the third time "Marcellus" has visited the village now. Luka explains that he is not his Marcellus; he is his son. But the Marcellus the youth remembers is too young to have a child at Luka's age. Promestein promptly asks what year it is, to which he replies it's the year 1430, by Johannes calendar.
Luka asks when the last time Marcellus was in the village was. The youth explains that the first time was a month ago. Marcellus looked full of life, and he had three companions with him. He still looked young. The second time Marcellus turned up was a week later, but he was alone and looked like an entirely different person. More like a seasoned veteran. The village chief also mistakes Luka for Marcellus. He mentions that he missed Marcellus the first time, but he managed to meet him on the second occasion. He recalls how they talked about the Tartarus and other odd events. Marcellus had also mentioned that something will happen in the next few years and that the villagers should leave before then. Marcellus had also asked the chief to give a letter to a boy named Luka if he ever showed up. But Ilias points out that shouldn't be possible, as this world's Marcellus is too young to have Luka. Luka asks the chief for the letter, after explaining that he's Luka. The chief hands him the letter: "To my son, Luka. If you're reading this letter, it means that I haven't returned to Iliasville. Most likely, Lucifina isn't with you anymore either. If she were, she'd never allow you to leave on an adventure. Please forgive your parents for not being there for you at such a crucial stage of your life. Seek Micaela's help, Luka. She lives in the hidden village of Enrika, deep inside the lost woods. Micaela should be able to help you, if anyone can. I'm determined to drive out the darkness that's covering the entire world. Go to Micaela and protect your world. Know that I'm proud of you for making it this far. -your father, Marcellus."
The party realises that the letter is not from this world's Marcellus, but the Marcellus from Luka's world, his actual father. Ilias is puzzled that members of Luka's family are capable of opening spacetime doors, but she cannot. By this point, Marcellus has left this world, as the letter was written to Luka over a month ago. The next letter is found in the Underground Library. Luka ventures into the Underground Library in the hopes of finding the book his dad left for him; The Four Animists and their Sources. Towards the back of the Underground Library, Luka encounters a monster who possesses books, going by the name of Page 65537. She knows Luka is searching for the book and informs him that she cannot allow him to have the book, by order of the Monster Lord. Ilias knows that it can't have been the 16th due to her sealed form, so it must have been the 15th. After the fight, she drops the book Luka needed. Inside of it is a note Marcellus left for Luka, "Luka, form contracts with the four spirits. By following the correct history, you'll suppress chaos in the flow of time". Luka is naturally confused, but Promestein finds it very intriguing. Ilias explains to Luka that he must have formed those contracts in the correct history, and following that history will suppress chaosization. Marcellus is first seen at the very end of Part 1. Before Luka and the party can leave the third Tartarus world, Adramelech appears and blocks their way to the exit. Her battle with La Croix knocked her down to only 10% of her normal power, so that gives Luka a chance. Defeated, Adramelech collapses, presumably dead. Luka and the party run through the exit, as the world falls apart around them. But Adramelech isn't quite dead yet. Her damaged form grabs Luka as they're running across the bridge back to their world. She's determined to drag Luka down into the "nothingness" with her. Luka believes this is the end for him, but a figure teleports into the dimension and cuts her in half with a sword by using Flash Kill, an angelic technique. That person turns out to be Marcellus. Luka's father. The family reunion doesn't last long. Marcellus explains to Luka that while he is trying to save one world, Marcellus is trying to save them all. He leaves the dimension through a conjured portal.
On the Alice route, at the very end of the chapter, Morrigan receives a telepathic message from her sisters. She learns that Alice XV has been killed by Marcellus and reveals this to the rest of the party.