Thank you for your question.
I’m not sure that SharePoint TOC web part is what you are looking for. It displays navigation of current site, not of the wiki document library.
The Knowledge base in Plumsail HelpDesk is just regular pages library. If you want to create table of contents on a page, you can edit this page and add links to appropriate pages in the text editor.
As an alternative, we suggest you to use OneNote as an internal knowledge base of your help desk.You can update right navigation and set link to the OneNote notebook instead of pages library.
If you need more functionality we also offer an ability to order improved knowledge base in our customization store.