I only read 2 chapters earlier and completely forgot to bookmark it, but as in the title, they end up in a sci fi world, but they end up in different locations. The boy gets trained by a woman (can't remember what she looked like) or the MC for that matter.
Man, you didn't give us much to go on. It would help if you could squeeze out more details.
However, the closest thing I can think of to what little you've got is Girl and Science:
It's not really a sci fi setting. it's more like a sci fantasy setting. Here's the description on Mangaupdates:
"They were childhood friends, and she had always been more powerful than him. But when they accidentally travelled (summoned?) to another world, it was finally time for him to become the knight in shining armor! He had to find her first though, since they were separated... Come and witness his fight to be better in a crazy world where monsters roamed and technology was so advanced your amputated limbs be restored to perfection..."