His Old Trafford reign will mostly be remembered for a long and spectacular series of battles with club record signing Paul Pogba.
It is that relationship which has come to define the Special One's time in charge at the club, with Mourinho never seeing eye-to-eye with the outspoken superstar.
Pogba's relationship with Mourinho was fraught from the moment he signed at the club, with the old school, disciplinarian approach of the Portuguese never fitting with brand Pogba.
That tension spilt into the public domain in September, when TV cameras picked up an astonishing training ground clash between the pair.
Here, we look back on the spectacular series of arguments that ultimately saw the Manchester United board side with their star player over their star manager.
According to a report in the Daily Mail, Mourinho was unimpressed with Pogba before he'd even properly returned to Old Trafford.
The French midfielder joined from Juventus for a then-world record £90million to massive fanfare.
Pogba's social media and marketing presence was clear from the off – an expensively produced video, featuring rapper Stormzy, announcing his return quickly went viral, while the hashtag 'Pogback' was created.
It was a massive social media coup for the club and one of the most Tweeted hashtags ever created.
Despite positive words in the media, old school Mourinho – who has also believed in the mantra that no player is bigger than a club – was apparently not so impressed.
The Portuguese has had concerns over Mourinho's attitude ever since.
2) Miami rehab
The first season passed without a huge amount of incident, with Pogba describing Mourinho as a "special" manager after they won the Europa League and the FA Cup.
There were some clashes during the season, with Mourinho concerned at Pogba's inconsistent form and distractions off the field.
It was at the start of the second season when the trouble really started.
In September, Pogba picked up a hamstring injury.
But rather than spend time rehabbing in Manchester, Pogba instead left for Miami, where he spent just over a week in recovery.
Mourinho was unhappy that the midfielder hadn't remained at home.
3) Sideline spat
The pair had a big argument at Wembley Stadium in January when Pogba was hauled off by Mourinho with the club losing against Tottenham.
A week later he was dropped from the starting line-up against Huddersfield Town and then hauled off again during the game against Newcastle United.
4) Dropped for the Champions League
Back in February, Mourinho made a massive call to leave Pogba out for United's two biggest games of the season.
Frustrated by the his inconsitency and lack of form, Mourinho left Pogba out for the first-leg of the Champions League last-16 clash with Sevilla.
An injury to Ander Herrera meant Pogba came on with less than 20 minutes played, but two weeks later, Pogba was again left out of the starting XI for the second leg.
United put in one of their worst performances in recent memory, losing 2-1 at Old Trafford.
The club crashed out of the Champions League and any chance of silverware that season went up in smoke.
Reports in the aftermath of that game was that the pair were not on speaking terms and would only communicate through assistant boss Rui Faria, who left the club over the summer.
5) Pardon the interruption
During a post-match TV interview after beating Liverpool 2-1 in March, Pogba deliberately interrupted Mourinho with a handshake.
The Portuguese laughed it off for the cameras, but later gave Pogba a dressing down in private.
Mourinho saw his antics as disrespectful.
6) Raiola revelations
Pep Guardiola revealed ahead of the crucial Manchester derby in April that super-agent Mino Raiola had offered Pogba to Manchester City in January.
Pep revealed: "Two months ago he (Raiola) offered me (Henrikh) Mhikitaryan and Pogba to play with us.
"He was interested in Mhikitaryan and Pogba to play with us. Pogba is an incredible player. A top, top player.
"I said no. We don’t have the money enough to buy Pogba because he is so expensive."
Pogba responded with a brilliant performance and two goals that stopped City winning the title against their rivals.
But the news was hardly welcomed by Mourinho that Pogba was being shopped to Europe's biggest clubs.
7) Pogba admission
Speaking at the end of last season, Pogba admitted that he and Mourinho were not that friendly.
"A coach and a player don't have to be best friends, we don't have to go to restaurants together," he said.
"I had a few little problems too… football is sometimes all about the mental side.
"He put me on the bench and I gave my response on the pitch. I always give everything I've got.
"He made me progress in leadership.
"I had the armband with Mourinho, it was the first time in a club, it's important for me, it makes me grow to be also a leader in the France team."
8) World Cup praise?
Pogba starred for France during the World Cup, as Les Bleus won the tournament in Russia.
But Mourinho wasn't completely enthusiastic in his praise – his comments coming across a little backhanded with Mourinho hinting that Pogba is easily distracted.
He said: "I think the World Cup is the perfect habitat for a player like him to give [their] best.
"Why? Because it's closed for a month, where he can only think about football. Where he's with his team on the training camp, completely isolated from the external world, where they focus just on football, where the dimensions of the game can only motivate."
Pogba later said: "We have a pure coach-player relationship, that's right.
"One thing I can assure you: I will always give 100 per cent, no matter which coach I always give everything, I cannot say more."
9) Barcelona calling
During the summer, before a brief reconciliation with Mourinho, Pogba told Ed Woodward he wanted to leave Old Trafford to move to Barcelona.
United were determined to keep hold of the Frenchman and rejected any transfer talk from the Catalan club.
But the news still reached Mourinho, who was understandably furious.
Negotiations were so advanced that Raiola and Pogba had even agreed personal terms on a contract with Barca.
SunSport revealed in August that Raiola had demanded a wage hike for Pogba to stay in Manchester – from wages of £180,000-a-week to £200,000-a-week.
10) Early problems
It only took one game of the new season for Pogba to make cryptic comments about his unhappiness under Mourinho.
Speaking after the 2-1 win against Leicester City, he said: "If you’re not happy, you cannot give your best."
Then when asked further what happiness would be, he added: "There are things that I cannot say otherwise I will get fined."
Mourinho was not happy with the comments and told him: “If you wish to leave Manchester, again, all you have to do is ask for a transfer”.
According to the Mail, Mourinho has also been concerned with the way Pogba arrives and leaves the team hotel.
Manchester United stay at The Lowry in Manchester the night before games and Pogba has taken to being dropped off to the hotel in a chauffeur-driven Rolls-Royce.
Further annoyance came after the win at Burnley.
Rather than return on the team bus with the rest of the squad, Pogba left Turf Moor in his chauffeur-driven Roller, heading straight to the airport to meet up with the French squad.
With some positive feeling returning to the squad on the back of a three-game winning run, there was real drama against Wolves.
Pogba had put in a man of the match performance against Young Boys on Wednesday night, scoring twice.
But Mourinho is said to have been annoyed with him before the game even kick-off.
One report claims that the Special One and the coaching staff were annoyed with Pogba for playing loud music on the team coach on the way to the game.
Mourinho wanted to create an atmosphere of focus and that was not the case.
Pogba had a poor game against Wolves and was caught in possession in the build-up to the equaliser – with the Portuguese manager also incensed at Pogba's reluctance to track back.
SunSport's Neil Custis revealed earlier this week that Mourinho blasted Pogba in the dressing room after the game for the error, which lead to Pogba's outburst post-game.
Mourinho is reported elsewhere to have told Pogba: "You're a good player, not a special player."
13) 'Attack, Attack, Attack'
Pogba made another high-profile dig at Mourinho's playing style and tactics after the 1-1 draw.
Speaking after the game, he said: "We are here to attack. Teams are scared when they see Man United attacking and attacking. That was our mistake today.
"We were winning 1-0 so it was positive for us.
"Then we tried to defend a bit more against the counter-attack.
"We stopped playing forward like in the first half and we didn't really put them in trouble.
"We are at Old Trafford and we should attack and press like we did against Tottenham, Liverpool, Chelsea and Arsenal last season.
"When we play like this it's easier.
"I can't tell you because I'm a player. It's not me.
"I am not the manager, I cannot, like, say that, but obviously we should show more options of playing.
"But I cannot say that, because I'm a player. That's my way of thinking – we should move better.
"We should move more, yeah."
14) Stripped of the vice-captaincy
Fuming with his performance and posturing, Mourinho made a power play to wrest control from the midfielder.
In the build-up to the Derby defeat, Mourinho told Pogba he would never captain the club under his watch again.
The move was made in front of the whole squad.
Mourinho claimed: "No fallout at all, no problem at all, just a decision that I don't have to explain."
15) Programme notes
In his notes for the game with Derby, Mourinho made a thinly-veiled dig at Pogba and some of his under-performing stars.
He wrote: "[The game against Wolves was] an important lesson; a lesson that I repeat week after week after week, a lesson that some boys are not learning.
"Every team that play Manchester United are playing the game of their lives, and we need to match that level of aggression, motivation and desire – 95 per cent isn't enough when others give 101 per cent."
16) In the stands
Hours after being stripped of the captaincy, Pogba appeared in the stands at Old Trafford.
Against the club's usual policy of wearing smart, conservative attire or the club tracksuit, Pogba appeared in a bright white tracksuit with his hood up.
Hardly keeping a low profile.
On top of that, Pogba posted a video on social media that shows him, as well as Andreas Pereira and Luke Shaw, laughing during Manchester United's defeat to Derby County, before seemingly leaving early.
The video was posted at 10.35pm, although it was recorded an hour earlier but couldn't be posted because a problem with the WiFi.
17) Training ground bust-up
The training ground video has brought everything to a head.
The clip shows Pogba arriving to the training pitch with a big smile on his face, before shaking hands with coach Michael Carrick.
Mourinho then makes a comment that clearly takes Pogba by surprise.
The two men are clearly bickering over something, with Pogba seen pointing to himself and saying "why me?"
SunSport revealed that Mourinho was furious with Pogba for the Instagram video.
Mourinho is understood to have found it disrespectful to other players who fought back from a goal down, with ten men, to force extra-time and penalties.
He can be seen asking media officer John Allen what time the video was posted.
Pundits suspect that Mourinho was fully aware the cameras would be recording and made another power play for the watching world.
18) 'You want me dead?'
Two days after the training ground bust-up, United put in a shocking performance at West Ham, losing 3-1 at the London Stadium.
Pogba was hauled off in the second-half.
In the mixed zone after the game, journalists attempted to get a reaction from Pogba – but the Frenchman replied with just four words: "You want me dead?"
Just in case it wasn't clear that Pogba had been gagged by the manager, he made it obvious a few nights later after a poor 0-0 draw against Valencia.
The midfielder said: "I've been told I'm not allowed [to talk]."
19) 'Delicate' situation
Later that week, Pogba's agent described the situation between his client and the club as "delicate".
Hardly a ringing endorsement that the Frenchman was happy at Old Trafford.
He claimed that the midfielder was not for sale at that time – but then in November, Raiola was reportedly in Italy to chat to Juventus over a potential return for Pogba to Turin.
Raiola and Mourinho have a fraught relationship, with the pair also at loggerheads over another Raiola client, Romelu Lukaku.
20) Pogba the 'virus'
The beginning of the end?
After a listless performance in the 2-2 draw against Southampton, Mourinho and Pogba had an almighty argument in the dressing room.
Mourinho even went so far as to describe the midfielder as "a virus".
He is alleged to have said: "You don't play.
"You don't respect players and supporters. And you kill the mentality of the good honest people around you.
"You are like a person with a flu, with a virus in a closed room – you pass that virus to the others."
As if that was not enough, the reaction from Pogba will only have made things worse.
As SunSport revealed, he 'laughed off' the criticism and told Mourinho he can't him for all of the problems at the club.
21) Valencia reaction
The Southampton game was the last Premier League game Pogba started under Mourinho.
He was dropped for the 2-2 draw against Arsenal, coming on for the final 15 minutes, and then didn't get off the bench for the 4-1 win against Fulham.
With United already through in the Champions League, Mourinho recalled Pogba to the starting XI for a dead rubber against Valencia.
In the build-up to the game, Mourinho said he wanted a reaction from his players… but was disappointed with the way they played.
He said after: "I didn't learn anything from this game."
"I expect (better) from my players, especially players that week in, week out, you ask me 'why don't they play?', 'why they don't they start?'"
22) Liverpool defeat
Again Pogba sat on the bench for Manchester United's biggest game of the season, at Liverpool on Sunday.
The French midfielder, the club's record signing, sat idly by as Liverpool smashed the Red Devils, winning 3-1.
Pogba watched as Mourinho started with a midfield three of Nemanja Matic, Ander Herrera and Jesse Lingard, and stayed on the bench as Marouane Fellaini came on ahead of him at half-time.
It was a poor defeat that left United 19 points behind their rivals, who lead the Premier League.
Mourinho was asked if he ever considered starting Pogba for the game.
He replied: "No.
"Because I am happy with Matic, Lingard and Herrera."
It was a kick in the teeth for Pogba and, perhaps more importantly, a final straw for Ed Woodward and the United board who had to see their £89million investment rot on the bench.
Mourinho may have been safe for another couple of months – had the Champions League draw not seen them drawn against French champions Paris Saint-Germain.
With little to play for in the league and slim hopes of progressing in Europe, time was up for Mourinho.
Pogba won the war.
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