I would say something like this should work. I don't have a linked server of any kind on my system so I can't test it:

SELECT

dept = e.dept,

fname = e.fname,

lname = e.lname,

empnum = e.empnum ,

calls_key = oq.calls_key,

ext = oq.ext

FROM

linkedserver.dbo.EMP e

inner join OPENQUERY(PHONEDB,'SELECT calls_key, ext FROM calls') oq

on (e.ext = oq.ext)

WHERE

e.ext = ext

AND e.active = 1

and oq.calltype IN ( 'from-internal', 'ext-local', 'ext-queues', 'ext-grou')

Also, please note the use of the table aliases especially on the linked server. The use of 3 and 4 part names in the select list is a deprecated feature and should not be used. You should use table alaises in the from clause.