Heero does know what it means for Altron knowing that Wufei is here, as opposed to what it might mean were Wufei not present. That's fine. There are a hundred other space-worthy ships in the hangar which he can use for the task, as Heero understands it.

His initial response to Wufei is a long, heavy pause. He isn't sure whether he should be here. But here he is, and Heero has been mulling over his options ever since. His gut told him that he should answer 'yes' - that this so-called opportunity presented by SUPERBIA wasn't something that he was allowed to pass up - but that doesn't mean Heero had planned very far ahead.

Now what?

Well, this appears to be some kind of shipyard.

"I'm going to find a ship," Heero says.