Symptoms

• You can see and click on "Tools" in Confluence page but the menu/options are missing. 
• Enabling Plugin Safe Mode didn't make any difference
• The problem persists even if you are using the default theme with no existing customization e.g. layout, stylesheet 

Diagnosis

Run the following query to check if confluence.content.action.menu is set to false in the database:

select * from BANDANA where BANDANAKEY='plugin.manager.state.Map';

If the result is returned with something like below, proceed to the resolution section:

...
...
<map>
<entry>
<string>confluence.content.action.menu</string>
<boolean>false</boolean>
</entry>
</map>
...
...

Cause

confluence.content.action.menu (Content Action Menu Sections Add On) which is a system/bundled plugin is set to false in the database

Resolution

Update the database (BANDANA table) and set confluence.content.action.menu to true and restart Confluence:

update BANDANA set BANDANAVALUE='<entry>
<string>confluence.content.action.menu</string>
<boolean>false</boolean>
</entry>
</map>' 
where BANDANAKEY='plugin.manager.state.Map';