Watson return creates selection headache
Although Watson remains the vice-captain and is almost certain to lead the side if Clarke is ruled out, his batting form has been disappointing for some time and strong performances from Steven Smith and Phillip Hughes in Mohali would make either of them unlucky to be dropped.
These are the questions faced by Clarke, the coach Mickey Arthur and on-duty selector Rod Marsh when the team begins training in Delhi on Wednesday, ahead of the fourth Test, which starts on Friday. Watson will be back with the group having flown home for the birth of his first child, but his trip home was also controversial because of his comments about being one of four players axed for the third Test for disciplinary reasons.
When he left Chandigarh, Watson said he considered the punishment "very harsh" and he would use his time at home to weigh up his cricket future. But after the birth of his son Will, Watson has reconciled with Cricket Australia and decided to rejoin the tour. Despite all of Cricket Australia's assurances that everybody is now on the same page, Watson's return could lead to some tension given his emotional comments on leaving India.
"I am very comfortable that Shane has accepted the punishment," Arthur said on Tuesday. "We have had a lot of conversations over the last week and they have all been very good. He didn't agree with the penalty but he agreed that they had done wrong. We have pretty much got that sorted and we have had numerous conversations and I am really comfortable with where it sits with Watto, we are really happy to have him back.
"I've spoken to Watto a lot, he has been incredibly supportive of where this team is moving to and really wants to be part of it. Once the emotion went away from Watto, he was very, very supportive of what we want to do with the team."
The main question now is how Australia can squeeze Watson into the batting line-up, given the success of Smith and the way Hughes fought through his spin demons in the second innings in Mohali. By contrast, Watson has averaged only 25.20 since taking over the Test vice-captaincy, which Arthur conceded was a concern.
If Clarke is ruled out the likely scenario is a straight swap with Watson, but if Clarke plays then the possible combinations become harder to determine. There are also decisions to be made around the bowling attack after the decision to send Mitchell Starc home for ankle surgery, but given Watson is not bowling on this tour his place can only be considered in the context of the top six.
"We haven't given it a thought yet," Arthur said. "We are really happy to get Shane back. It is really important he came back. Shane's been exceptional over the last week we've had numerous conversations with him. In terms of selection there are a couple of variables right now, Pup's back and Starcy going home. We'll sit down once we have a look at conditions and we'll get it pretty much sorted tomorrow.
"Watson's form is a concern. He looks like he's going to get runs every time he goes to the wicket, he just hasn't kicked on. Watto is the first one to admit that he needs a big score, there's no doubt about that. I'm backing him in to get one pretty soon and then hopefully when he gets it, that just opens the floodgates for more and more runs."
Arthur confirmed that despite the events of the past week Watson remained the vice-captain and likely candidate to lead if Clarke does not play in Delhi. He said that would be a decision for the selectors on duty. Arthur is one of those three selectors while another is Clarke, who said after the Mohali Test he expected Watson would lead if he could not play.
"I am comfortable that if Pup doesn't come up he could do the job," Arthur said. "That could be a discussion with the other on-duty selectors as to what we did but Shane at the moment is vice-captain. You would have to assume that because he is still the vice-captain that we probably wouldn't go past him, but again that would be a discussion."
Arthur said it was impossible to rule Clarke out given the way he has managed his ongoing back injury in the past - he has never missed a Test because of it - but he said Clarke's place in the team would not be decided until closer to the match.
"He is in a bit of pain," Arthur said. "With Michael Clarke you never say never. He will give himself every opportunity to get himself ready for the Test. That will pan out closer to the time and will give him every opportunity to get up for it because he is such a vital cog in our team."
Brydon Coverdale is an assistant editor at ESPNcricinfo. He tweets here