But what next?
The dream when the fan-owned club rose from the ashes of Chester City in 2010 was to be back playing in the Football League within 10 years.
Few will be expecting a promotion push next season.
But, after what hopefully looks like being a campaign of consolidation, what can the Blues do, both on and off the field, to progress in 2017-18?
Here's what our fans' jury members had to say...
"It's a shame that the season appears to be petering out to what would be a disappointing end. A season that, up until Christmas, offered so much hope and genuine signs of progress. I believe that the fans and squad alike bought into Jon’s philosophy of a strict 4-4-2 system with everyone understanding their role and what was required from them. Unfortunately injuries and, at times, over-ambition have led Jon away from this mantra and have exposed the limitations of our small squad.
"Year on year this league is becoming more physical. Just look at the likes of Lincoln, Tranmere and Forest Green, sides who have players capable of asserting themselves in all areas of the pitch. Therefore, if we look back to ourselves, it's no surprise that fans have highlighted the likes of Sam Hughes, Ryan Astles, James Alabi and Tom Shaw as stand-out performers this season. All big lads capable of mixing it at this level.
"I admire Jon's conviction and belief that as a coach and mentor he can gain further improvements from the current crop of players, but to kick on next season I'd like to see two things happen come the summer.
"Firstly, we need to ensure that we can get full value from what will inevitably be another small squad and this unfortunately means moving on those players who have spent significant periods of the season out injured. Secondly, I'd like to see us add a greater physical presence in all positions. This is especially important when you consider that there's a reasonable chance that two of the previously mentioned names will no longer be with us when we kick off the 2017-18 season.
"If we can do this, then there's no reason not to believe that we can have a solid, competitive season next time around. Let's not forget that Jon is new to the manager's role and I'm sure that this first full season will have been a sharp learning curve for him personally and one that he'll be all the better for.
"After that, it's a case of getting things right off the park and developing the income streams that hopefully, a few years down the line, will give Jon the funds to make us genuine play-off contenders. COYB."
"We need some new blood into the squad to give some competition for places. If we had a bit better squad depth this season I feel we really could have kicked on and had our best ever finish.
"More needs to be done off the pitch also as it seems we are just going backwards and, considering we have hired someone to look after off-the-field affairs, and also to get people through the gates, it's not happening. For example, we could have done an offer on the last remaining home games to give the lads a boost and get us over the line.
"Also, with the way the results have been going below us, we are definitely not safe yet and with hard games coming up we could get sucked into trouble. York and Woking at home are key games and I believe if we win one of those then we will be fine but it's a bit worrying considering where we were at Christmas.
"My worry is, with the obvious players moving on, and the new teams coming up having decent money to spend, we could be at the wrong end of the table. I really hope I'm wrong and Jon builds a competitive squad and we kick on next season."
"On the pitch I'd like to see us make sure we have enough options in each area, I think this has been an increasing problem as the season has gone on. We've not really had many attacking options since October when James Akintunde picked up his injury and have just tried to survive with two strikers since. Similarly at the back, if Theo Vassell has missed any games we have had to slot numerous players in at right-back at times.
"We've been a bit unfortunate with injuries but that certainly needs to be taken in to consideration when offering new deals out for next season. We're likely going to have to contend with another small squad, after all.
"Off the pitch, well you can't get away from the fact that we've struggled to get people in this season. This needs to improve so hopefully some plans behind the scenes come to fruition. Whether it's down to the cost, a poor run since the halfway point in the season, the slightly defensive and disciplined set-up we go with on the pitch, or something else.
"Fortunately, the struggles in that area this season might be financially offset by some transfer fees in the summer. But it's not income you can get accustomed to and expect, though."
"For Chester to 'kick on' next season, the club needs look at three key issues.
"Firstly, the alarming slide in attendances needs to be halted. It would be hard to justify any price increases so someone at the club needs to devise some kind of an initiative to increase gates. I know there is all this talk about the mythical 'floating fans', but the club shouldn't be chasing these people as they can just as easily float off.
"Jim Green is working wonders at the Community Trust by engaging with local schools and we should have more games next season where schoolchildren and their parents can apply for discounted tickets. These kids are the next generation of committed fans.
"Access to the ground from the city centre is not easy, especially for those without transport. Poor transport links are a real barrier to fans attending and I've always thought the club, in conjunction with CWaC, should be looking at utilising the Sealand Road Park & Ride to allow fans a quick and easy means of getting to the match. Can we not explore this option?
"Secondly, we need to invest in the infrastructure at the club. Fingers crossed we get a substantial six-figure fee for Sam Hughes and this money should be invested wisely. After this season's financial black hole has been filled and Macca has been given a few bob to spend on the squad, we need to invest the remaining monies wisely; either at the ground to improve the matchday experience (a semi-permanent marquee like Tranmere's 'fans zone' would be nice), towards new community based training facilities (a useful source of income) or investing further in the academy.
"Lastly, Chester really needs to explore and exploit all possible income streams. In a season where we've taken a financial hit, it really concerns me that so few fundraising activities have taken place. Something like a Christmas Raffle, properly supported by the club, could have easily raised £7,000, a figure that would make a significant dent in the projected losses. At the same time our supporters need to realise that running a National League football club is an expensive business, so please help out if you can, don't wait to be asked."
"To an extent I think we need to be at a level where we can kick on financially. With Sam Hughes nailed-on to leave, we will hopefully receive a tribunal worth a vast amount of money.
"Jon McCarthy has already conceded that we will have a tighter budget next season, possibly with less players. Consequently, any money received from a Sam Hughes transfer needs to be spent wisely on our squad. Maybe we need a couple of more strikers, or targetmen to be precise. And in case something disastrous happens, maybe we need one or two defenders who can play the Sam Hughes/Ryan Astles way, or maybe we could add some more depth in midfield. If key players go, we could gain some more talent.
"With teams such as Salford and AFC Fylde possibly to come into our league and a big club such as Leyton Orient (if they don't become extinct) possibly coming down with parachute payments, life in the National League might become tougher.
"We have fought well this season and not many people would have predicted us to be in this position. To be where we are at and defeating teams with massive budgets is impressive.
"If we, as a club, learn from past mistakes, I have no doubt that we can kick on next season. COYB."
If you would like to become a Chester FC Fans' Jury member you can email firstname.lastname@example.org.