Weird misalignment on only one part of the model  

It looks like, despite the brim, the free standing handle was just beginning to sag when it reached the joining bridge.

You may be lucky with a reprint or you might have reached the point at which the accumulated weight naturally takes charge.

If you can do so I suggest chamfering the shoulder of the handle and then printing this upside down; check the bridging looks sensible before printing.

Cheerio,

Weird misalignment on only one part of the model

Thanks for the suggestion.

I noticed that the model author included a version that connects the handle to the larger base at the bottom. I was thinking it might've been just aesthetics but now I notice the name of the STL is _BedAdhesion so perhaps this is a common problem with this model.

I'll try reprinting with the attached version and then worst case I can just cut off that connection to get back to this version.

Leveraging part momentum for tall parts

The other thing you can do with a model like that which has two parts that merge at the top is minimize the impact of momentum during the print.  Left to right movement of the head (X axis) is preferred to back and forth movement of the bed (Y axis) - from what you show here, I'm guessing the handle was oriented towards the front or back of the printer.  With that orientation, you could add a part to the print for later removal that braces the lateral movement of the handle while it is free standing.  A triangle piece that just barely touches the handle would be a good brace.   Upside down would be another option.  Reorient for momentum prevention is another.