Jefferies and Johnston had a difficult relationship
By Chick Young BBC Scotland football correspondent
Prayers for Kilmarnock may be all that is left, but I'm not convinced the good Lord will be listening, for this is the unholiest of messes now.
Wars are an evil business at the best of times: civil ones leave a particularly bad taste in the mouth. And there sure are some fires burning behind the drawbridge at Rugby Park.
For several months, those of us privileged enough to be allowed to walk the corridors at this once friendly and welcoming club, for whom I have always embraced a warm spot in my heart since Mr Willie Fernie - an awful nice man - was the manager in the seventies, have been aware of a strange unease.
It exploded spectacularly with Kevin Kyle's allegations that the chairman was criticising the manager's tactics. The captain turned out to be a clipe.
The chairman, meanwhile, claimed he spoke with forked tongue.
But please don't be fooled into thinking that this was the beginning of the troubles. The blue touch paper was trying to seduce anyone with a light for months.
And now Jim Jefferies, whose eight years at the coalface equates by current managerial standards to a lifetime of devotion, has gone, his trusted lieutenant Billy Brown riding by his side into the Ayrshire sunset.
Kyle's allegations brought matters to a head at Rugby Park
In truth, a fair percentage of the club's support will not be sad to see them go, for Killie have hiccoughed and coughed their way through the first half of the season and the natives have been restless for some time.
But Michael Johnston, the one-man board who seems to operate a dictatorship, hasn't exactly been pin-up material for he supporters either. At best, he has taken one outrageous gamble, at worst he will be running from the mob like Tam O'Shanter's horse.
Except, unlike the grey mare Meg, crossing running water won't be enough to save his soul.
Jefferies was running his team with one hand tied behind his back. No, hold on, he was handcuffed, blindfolded and gagged.
He lost the services of a coach, a chief scout, a doctor and a video operator. I suspect, although Johnston will say otherwise, he had also been left without the full belief of the chairman.
And now Kilmarnock, like Dundee United and Motherwell, seek a manager. The old merry-go-round is throbbing at last and would you rule against Jefferies and Brown rolling in to Tannadice or Fir Park?
And what now in Ayrshire? Will Johnston and his seemingly interfering ways scare off whichever man offers genuine hope of salvation for the tortured club?
The is not the Kilmarnock that made us smile, the cup winners of '97, or earlier in the decade the club dragged from the precipice by Bobby Fleeting's showmanship and entrepreneurial skills. Fleeting times: too fleeting actually.
They are a club now who have forgotten how to smile, living in fear of what relegation may bring. In their perilous financial state, there may ultimately be work for the Grim Reaper. The situation, my friends, is actually that black.
Kilmarnock Football Club have forgotten how to enjoy themselves.
Even the statement that told the world the manager had gone was cold and unfeeling. "By mutual consent," it said. I'll bet it was. They couldn't wait to see the back of one another and that tells the tale.
I said on BBC Radio Scotland's Sportsound on Saturday something would have to give. Johnston and Jefferies were in the middle of a massive domestic. Divorce was the only option.
This was hardly a statement of great insight and vision. It was depressingly, blindingly obvious,
Now the chairman has an unhappy dressing-room with which to deal. Oh, and the supporters don't seem to see the funny side of all of this either.
Are we really to believe that Jefferies has been sacked, oh sorry, left my mutual consent, because of the league position?
Was he not the very kind of experienced chap, well versed in the fight for survival, you want alongside you in the trenches in which Kilmarnock now find themselves?
Or was the rift between the chairman and manager - who had the full support of his players - just too wide?
Johnston has taken the weight of Kilmarnock's world on his shoulders. He had better have gotten this one right, but my real fear is that his judgement is wildly off the mark.
The biggest irony may lie with the Latin club motto, "confidemus" - we have confidence. Aye, right.
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