Since the day he was signed as a free agent in March, McKinnon was slated to be a significant piece in the complex puzzle that makes up Shanahan's offense. Now, that puzzle will have a bit of a different look.
"Since the day we signed him, we've been game planning for Minnesota," Shanahan said. "I'm not going to lie. It changes things pretty drastically. That was your first target in free agency, so once you do it, you know you have a plan on how to use him, especially going into Week 1. So that definitely changes but we didn't have him before, so we've done a lot of different things with that.
"We were going to do some different things with him, which we have other guys on the roster capable of doing that stuff, but it's just how much you want to do it and things like that. That changes formations and everything.
"We definitely had to go back in and change some things, but definitely still excited about what we've got."
McKinnon spent an entire offseason impressing Garoppolo, who praised the running back at every opportunity.
"It was tough (losing him for the season), especially in that situation," Garoppolo said. "It was the second or third play of practice, really. My back was to it, so I didn't even see it, really. But that sucks.
For a guy who works as hard as he does and puts as much as he puts in this team, it's tough, but we've got to move on. Injuries happen in this league. That's kind of part of it."
With McKinnon out for the season, running backs Matt Breida and newcomer Alfred Morris will try to carry the load. Shanahan has not decided who will start on Sunday against the Minnesota Vikings. Breida is returning from a separated shoulder he suffered during the 49ers' exhibition opener against the Dallas Cowboys.
"We'll see how the week goes," Shanahan said. "This is Breida's first full week back from his injury, so we've got to see how healthy he is. It probably depends a lot on personnel groupings, what plays we're running, things like that. I probably won't have an idea on that until Saturday night."
Neither Breida nor Morris are quite the versatile weapon that Shanahan envisioned having at his disposal with McKinnon. The head coach, however, isn't worried about opposing defenses assuming the 49ers will run the ball with either of them in the game.
"We'll be balanced in both (passing and rushing)," Shanahan said. "It's very rare you can have a guy on your roster who can't catch at all or can't run at all. If you're only catching passes, they can call you a running back, but you're a receiver. So you've got to balance all that out. We have the running backs who can do that. Guys do certain things better than others but all three of the guys that will be up, I feel confident all three of them can definitely run and catch."
Garoppolo started five games without McKinnon in the backfield last season, and he will spend at least 16 more this season without him. He does, however, have confidence in the remaining healthy running backs on the roster.
"Those guys (are) hard workers," Garoppolo said. "Me and Matt have been going since last year together. It's good to have him at full speed now. We've still got a good group back there."
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