• Colin Kaepernick #7 of the San Francisco 49ers warms up prior to playing the Los Angeles Rams in their NFL game at Levi's Stadium.

Colin Kaepernick #7 of the San Francisco 49ers warms up prior to playing the Los Angeles Rams in their NFL game at Levi's Stadium. (Photo : Getty Images/Ezra Shaw)

Colin Kaepernick finally met up with the new top honchos of the San Francisco 49ers – John Lynch and Kyle Shanahan. There were no details on what went down but the good news is that everything ended well.

With Colin Kaepernick, John Lynch and Kyle Shanahan parting on a high note, does it mean that the controversial quarterback is staying in San Francisco? For now, it may be too early to tell.

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At the top of the list is the contract of Colin Kaepernick. The 29-year-old could opt out and test the NFL free agent market though there is no assurance that he would get a similar or better deal, CSN Bay Area reported. Seeing how his past NFL seasons have gone, teams are likely to consider him but on a lower deal.

Should that be the case, the easy alternative is to stick with the 49ers to make sure he gets that $14.5 million contract. The problem is that all that was before the head rolled. With John Lynch and Kyle Shanahan now in charge, there is a chance that they counter with a contract restructuring or waive Kaepernick.

The alternatives don’t sound pretty but are a reality. The 49ers do need a quarterback but Shanahan already had some names in mind. The list includes Jimmy Garoppolo, Matt Shaub, and Kirk Cousins, according to a report from ESPN. Right now, there is no movement but other teams are eyeing these players as well.

If so, Kaepernick could be the backup plan for Shanahan just in case. But is he fit for the offensive system that the new coach has in mind?

Based on his past performance, Kaepernick should be an easy fit for as long as he syncs in with Shanahan. Consistency is another matter to consider, not to mention focus. Kaepernick made headlines last year with his antics – particularly the one where he took a knee when the national anthem was played and wearing a Fidel Castro shirt.

If not among his list or Kaepernick, Lynch and Shanahan could turn to the 2017 NFL Draft. They do own the second overall pick and could use that on DeShaun Watson – assuming the Cleveland Browns pass and take defensive end, Myles Garrett, instead.

Check out the video below weighing in on the possibility of seeing Kaepernick as the 49ers starting quarterback next season.