Rufus was married to Fatima while he was working at RTASA. He never mentioned her while he was alive, and nothing is known about his sentiment towards her.
Weller assisted the Vanguard in their war against the Union, but was very irritated when gen:LOCK became militarized and thus altering its original goal.
Weller served as chief scientist of the ESU, and within it developed gen:LOCK as a means of advancing humanity as a whole. He worked on said goal for the rest of his life while in the ESU.
Caliban was Weller's first attempt at creating gen:LOCK technology. He stored all of his plans, designs, and ideas for the project within Caliban's memory. In the likelihood of his death, he imparted protocols that would have Caliban allow the gen:LOCK team to access the information. Weller had also had a partial copy of his own mind into Caliban's prototype version of the mindframe. However, he found Caliban's attempts at humor to be lacking, hence why he kept the android muted most of the time.
Chase was on good terms Weller, and appeared grateful to him for saving him and the giving him an opportunity to serve in the gen:LOCK program in spite of his condition. Weller, on the other hand, felt a responsibility for Chase, and had great pride in the latter's successes early on in gen:LOCK. However, when Chase's Holon was captured by the Union with his mind still trapped inside it, Weller felt a great deal of guilt for not being able rescue him. When it was decided that a compiled copy of Chase's mind was to replace the one lost with the Holon, Weller expressed relief, but felt even more guilt for hiding the truth.
When it became clear that Nemesis was in fact Chase's original mind. Chase confronted Weller and was angered and embittered by the doctor's explanation. Faced with an existential crisis, Chase brushed off any attempts Weller made at apologizing, and never interacted him over the course of the Union's assault on the Anvil, in which Weller died. Eventually, following Weller's death, Chase came to terms with his identity and appeared to have forgiven Weller.
Weller is taken by surprise when he first encounters the spy and is quickly captured by him. After some discourse, Weller realizes the spy is not Rob Sinclair and thus knows a way to stop. He pretends to acquiesce to the spy's demands for a Holon, fully aware that his lack of compatibility would've killed him. When the spy perishes attempting to upload, Weller shows no remorse over his fate.
When the original Julian Chase is abducted by the Union, Weller seemed unaware of what befell him. And then when Nemesis appeared, Weller realized it was actually Chase, modified and corrupted by the Union. He tried to reason with him during the Battle of The Anvil, but ultimately to no avail.