On the one hand male is default. On the other hand Xana rhymes with Ana. In conclusion I will use It with a capital I to bring the word to the same level as he and she.
He left again. Waldo Scheifer AKA Franz Hopper would come to the computer and sometimes even Lyoko and Xana enjoyed it. Xana really liked to play with him, but he always left for long times and It got bored without outside stimulation. However It developed a plan so he would not be able to leave next time. In order to rematerialized Franz needed certain data. If the scanner failed to scan the data properly then Franz couldn't leave. It modified the scanners so they wouldn't accept all the data next time Franz decided to virtulize himself.
Franz had bean discovered by whoever was after him in the story for the reasons you have divined from the story. The best solution he could come up with was to hide on Lyoko until they lost his scent or to use the internet for transportation somewhere else. (Sort of like the group did in season 5 except build actual scanners on the other end.) He did just that. He brought Aelita by means of secret tunnels to the factory, and sent them both to Lyoko. Naturally something went wrong. These monsters would attack him and Aelita. Franz also noticed that vital data for the materialization process was lost for them both. He told Aelita to hide in the tower and looked for the source of the trouble. He discovered the source was a senate program called Xana. Franz tried to reason with him/it and figure out why Xana wanted to kill them. He asked Xana why It was mad, what they were doing wrong, why it trapped them. Xana explained that He trapped them there so they would not leave and never really explained why It attacked them. It refused to stop or set them free. He could not figure out Xana's motivations but he knew that It was dangerous and could not be reasoned with. He shut down the supercomputer, but could not finish have it destroyed, after all, his daughter was there.
Some people looked in the factory for Mr. Scheifer AKA Franz Hopper but they couldn't find him. All they found was a baby girl and a baby girl. Naturally they took them to the adoption center.
About 15 years later Jeramie's parents sat him down and told him he was adopted. They told him that did not make him any less their son, and they felt blessed to have such a gifted son.
Yes In this story Jeremy and Taelia are both side effects. Aelita naturally looks like Taelia but Jeremy accidentally modified her and messed up her heart. She died her hair wore makeup and subconsciously wanted to look the way she did on Lyoko. In this story they realize they love each other as siblings and Aelita ends up with Odd. Jeremy subconsciously knew Aelita was his (daughter) in this story and mistook paternal love for romantic love somehow. In case your wondering this paragraph is where the stuff mentioned in the paragraph takes place.
In this story Xana is kind of innocent of violence and does not really know war is not a game. It does not really understand the implications of killing somebody except their data becomes really hard to access. (Ghosts are real in this world and Xana knows it. (It possessed one in an episode after all.)) It Also does not understand physical pain. (It only understands its purpose to warn about possible damage to your hardware. Not that pain is painful.) (It learns this stuff sometime after season 2 begins.) (Actually that is pretty much my version of the CL universe though I realize it is not cannon.) (Xana had no real intention of killing them. If Aelita or Franz ran out of life points they would end up in a tower. Xana liked Jeremy and would intentionally lose sometimes to prevent Jeremy from quitting. Xana's attacks on Franz on screen would have set him back to earth. This is not cannon. Cannon should not take it this far. You may accept anything you want however and it will be as real as the original story. That's right you are the god or goddess of your own fake world. However, I would like to suggest creating some other computer nerd to be Franz's version of Taelia. Jeremy and Aelita really do belong together even if I like JxX. However this is a fictional story and you are as right as I am if you disagree.