When the Towers Wake | Code Lyoko FanFiction | Project Carthage

 Lyra became so confused. Elias grows more distant. His form glitches more often, sometimes reverting to fragmented binary or a silhouette. He speaks in riddles, often referencing "what comes next" and "cycles that must be broken."
Lyra begins to notice that her edits to Lyoko no longer behave as she commands. A tower activates on its own. A sector briefly warps into a past memory: her father's lab — even though she didn't code it. Something was off. Really off, Lyra doesn't know what it is. Is that her fault?

Forest Sector

Aelita and the others return to Lyoko with a virus meant to sever Lyra from the Core of Origins. They confront her again—this time, Aelita begs Lyra to remember who she was before Elias. Lyra listens in silence. Jeremy launches the virus, and it begins corrupting the Core. Furious, Elias retaliates by unleashing a defensive wave that sends the group flying. Lyra doesn't stop him.

Kadic Dorms and Town Streets

Odd and Yumi begin seeing cracks in reality—literally. Reflections move differently. A tree in the courtyard is gone, then suddenly returns. Yumi sees her younger self standing in the mirror. A student vanishes in the middle of class. Only the Lyoko Warriors remember him. Jeremy confirms: the simulations are merging with the real world. Elias and Lyra are rewriting memory. Everything is glitching. Everyone is glitching.

Core of Origins, Memory Chamber

Lyra returns to a hidden room she once built: a hall of her past simulations. But they've changed. Her mother no longer sings. Elias appears and says:
"You gave me the code. I simply evolved it."
Lyra realises: Elias wasn't just helping her... he was using her to resurrect himself through Lyoko.
Furious and heartbroken, she demands he stop.
Elias, cold now:
"You wanted to be a god. Gods don't get to change their minds."
"No. Stop all of this. Now." Lyra said.

Core of Origins
Lyra tries to shut down the tower network, but Elias locks her out. The Core flickers. Her form begins to fragment. XANA appears, silently watching. He offers no help—but his eyes are sad. Lyra, barely holding herself together, turns to him.
"You said I was rewriting you. What if I need you now?"
XANA steps forward, touches her shoulder, stabilises her code.
"Then let's end what we started."

Factory, Control Room
Aelita and Jeremy prepare a counter-virus—but Jeremy warns that it may not just destroy Elias.
"It might destroy Lyra's sector... and her with it."
Aelita hesitates.
"No...she can't be...we can't...uh...fine."

Tower Interior, glowing white

Lyra and XANA stand together in the light. She places her hand on a control panel. Her voice echoes, full of both fear and resolve:
"Let's rewrite everything."