Defaulting missing data - sql

Question

I have a complex set of schema that I am trying to pull data out of for a report. The query for it joins a bunch of tables together and I am specifically looking to pull a subset of data where everything for it might be null. The original relations for the tables look as such.
Location.DeptFK
Dept.PK
Section.DeptFK
Subsection.SectionFK
Question.SubsectionFK
Answer.QuestionFK, SubmissionFK
Submission.PK, LocationFK
From here my problems begin to compound a little.
SELECT Section.StepNumber + '-' + Question.QuestionNumber AS QuestionNumberVar,
Question.Question,
Subsection.Name AS Subsection,
Section.Name AS Section,
SUM(CASE WHEN (Answer.Answer = 0) THEN 1 ELSE 0 END) AS NA,
SUM(CASE WHEN (Answer.Answer = 1) THEN 1 ELSE 0 END) AS AnsNo,
SUM(CASE WHEN (Answer.Answer = 2) THEN 1 ELSE 0 END) AS AnsYes,
(select count(distinct Location.Abbreviation) from Department inner join Plant on location.DepartmentFK = Department.PK WHERE(Department.Name = 'insertParameter'))
as total
FROM Department inner join
section on Department.PK = section.DepartmentFK inner JOIN
subsection on Subsection.SectionFK = Section.PK INNER JOIN
question on Question.SubsectionFK = Subsection.PK INNER JOIN
Answer on Answer.QuestionFK = question.PK inner JOIN
Submission on Submission.PK = Answer.SubmissionFK inner join
Location on Location.DepartmentFK = Department.PK AND Location.pk = Submission.PlantFK
WHERE (Department.Name = 'InsertParameter') AND (Submission.MonthTested = '1/1/2017')
GROUP BY Question.Question, QuestionNumberVar, Subsection.Name, Section.Name, Section.StepNumber
ORDER BY QuestionNumberVar;
There are 15 total locations, with this query I get 12. If I remove a relation in the join for Location I get 15 total locations but my answer data gets multiplied by 15. My issue is that not all locations are required to test at the same time so their answers should default to NA, They don't get records placed in the DB so the relationship between Location/Submission is absent.
I have a workaround almost in place via the select count distinct but, The second part is a query for finding what each location answered instead of a sum which brings the problem right back around. It also has to be dynamic because the input parameters for a department won't bring a static number of locations back each time.
I am still learning my SQL so any additional material to look at for building this query would also be appreciated. So I guess the big question here is, How would I go about creating default data in this query for anytime the Location/Submission relation has a null value?
Edit: Dummy Data
QuestionNumberVar | Section | Subsection | Question | AnsYes | AnsNo | NA (expected)
1-1.1 Math Algebra Did you do your homework? 10 1 1(4)
1-1.2 Math Algebra Did your dog eat it? 9 3 0(3)
2-1.1 English Greek Did you do your homework? 8 0 4(7)
I have tried making left joins at various applicable portions of the code to no avail. All attempts at left joins have ended with no effect on info output. This query feeds into the Dataset for an SSRS report. There are a couple workarounds for this particular section via an expression to take total Locations and subtract AnsYes and AnsNo to get the true NA value but as explained above doesn't help with my next query.
Edit: SQL Server 2012 for those who asked
Edit: my attempt at an isnull() on the missing data returns nothing I suspect because the query already eliminates the "null/missing" data. Left joining while doing this has also failed. The point of failure is on Submissions. if we bind it to Locations there are locations missing but if we don't bind it there are multiplied duplicates because Department has a One-To-Many with Location and not vice versa. I am unable to make any schema changes to improve this process.
There is a previous report that I am trying to emulate/update. It used C# logic to process data and run multiple queries to attain the same data. I don't have this luxury. (previous report exports to excel directly instead of SSRS). Here is the previous logic used.
select PK from Department where Name = 'InsertParameter';
select PK from Submission where LocationFK = 'Location.PK_var' and MonthTested = '1/1/2017'
Then it runs those into a loop where it processes nulls into NA using C# logic
EDIT (Mediocre Solution): I ended up doing the workaround of making a calculated field that subtracts Yes and No from the total # of Locations that have that Dept. This is a mediocre solution because I didn't solve my original problem and made 3 datasets that should have been displayed as a singular dataset. One for question info, one for each locations answer and one for locations that didnt participate. If a true answer comes up I will check its validity but for now, Problem psuedo solved.