INDIANAPOLIS -- There will be no more excuses for San Francisco's triad of head coach Chip Kelly, general manager Trent Baalke and quarterback Colin Kaepernick.

Baalke dispelled questions about Kaepernick's immediate future Wednesday during a news conference at the NFL Scouting Combine. Baalke said Kaepernick will remain on the roster after April 1, which means the 49ers will guarantee his $11.9 million base salary for the 2016 season.

While the 49ers could still trade Kaepernick elsewhere, Baalke strongly indicated that wasn't in the plans. Baalke envisions a competition between Kaeprnick and Blaine Gabbert for the starting spot entering Kelly's first season as 49ers head coach.

More from FoxSports

Distractions now aside, this means Kaepernick, Kelly and Baalke can both start getting to work in trying to salvage their respective NFL careers and reputations -- together.

It isn't going to work any other way.

Kelly has desperately needed a quarterback with Kaepernick's skill set to run the type of read-option packages that helped lead him to success at the University of Oregon. The only run-pass threat Kelly deployed the past three seasons during his ill-fated stint in Philadelphia was a 33-year-old Michael Vick, who wasn't nearly as spry as the younger Kaepernick is now.

Kelly then compounded the problem in 2015 by having a pocket passer (Sam Bradford) try to run a hybrid scheme that bombed with defenses not having to worry about a quarterback turning up-field. It now falls on Baalke to make sure Kelly doesn't make the same lousy personnel decisions that led to the Eagles fading from a double-digit win season to mediocrity.

In turn, Kaepernick has needed a system that can accentuate his athleticism and hide his limitations in reading defenses like ex-49ers head coach Jim Harbaugh and offensive coordinator were able to accomplish during the 2012 and 2013 seasons.

"If you look at the quarterbacks that (Kelly) has had, he hasn't had a bunch of guys that can run," Baalke said. "He's been able to put together some pretty good offenses with guys that aren't able to run. You get an extra advantage of having a quarterback that can run. I think if you talk to any coordinator, they're going to take that as a positive."

Kelly, Kaepernick and Baalke all desperately need some positive results in 2016.

Baalke must prove he can build another winner after the Jim Tomsula fiasco and gradual disintegration of the roster from the Halcyon days of Harbaugh's first three seasons with the 49ers. This will be Kelly's final NFL head coaching opportunity if he doesn't learn from the myriad of mistakes he made with the Eagles. And Kaepernick is fighting to prove that he is the franchise quarterback Baalke and the 49ers thought he was when re-signing him to a long-term contract extension prior to the 2014 season.

This scenario is one of the reasons Baalke is so anxious for the 49ers to begin their offseason training program in early April.

"Chip is excited to work with (Kaepernick) just as he's excited to work with all of these guys," Baalke said. "I don't think there's anybody on our team that has come over from Philly, so he has no working knowledge of any of these guys. He's just as excited as anybody to get out there and get going."

If the 49ers don't get going, it won't take long for Kelly, Kaepernick and Balke to be gone themselves.