Now the Colts are about to go head-to-head with another one of their issues when they take on the New England Patriots in the AFC Championship Game on Sunday.
Patriots quarterback Tom Brady is headed to the Hall of Fame once he retires, and yes, he's a handful to deal with, but the problem the Colts have had when they've played New England the past two times is stopping the run.
For the Colts, it started in the 2013 divisional-round playoff matchup when the Patriots rushed for 234 yards, including 166 yards from LeGarrette Blount, and then they had a repeat performance back in November when they rushed for 246 yards, including 201 yards from Jonas Gray.
"There's no way we don't know who their running backs are," Colts defensive lineman Ricky Jean Francois said. "We have statistics of their running backs very well. We know what we have to do in this game. We have to stop their running game. It's a must. It's like the Denver game, if we didn't stop the running game, it's hard as hell to stop a team that can run and pass the ball."
The Colts were embarrassed after that game in November. They hadn't given up more than 136 yards rushing to a team prior to that and then suddenly a player who hadn't rushed for more than 86 yards in a game ran around, past and through them.
The Patriots used an offensive scheme that featured a power look with a sixth offensive lineman against Indianapolis. They used six offensive linemen on 37 snaps in that game, daring the Colts to try to stop them. Indianapolis, obviously, failed over and over again.
"As a defensive player, you don't want to ever have that happen again," Colts defensive lineman Cory Redding said. "We didn't have our best game. It's up to us to do what we've done the past few weeks, to make sure that never happens again."
The Colts held Manning and the Broncos, who had become more of a run-oriented team with C.J. Anderson, to only 88 yards rushing last weekend. Now they'll attempt to do the same against the Patriots, who have proven they can be effective running the ball no matter who is in the backfield for them.
The Patriots rushed for only 14 yards against the Baltimore Ravens last weekend, but that's largely because they completely abandoned the running game in the second half. Their only attempt in the second half was a quarterback sneak by Brady because Baltimore was dominating them up front.
Redding and the rest of the Colts' defensive linemen have to do the same thing on Sunday.
"They execute, they block well, they open up holes, got good runners," Colts coach Chuck Pagano said. "We've got to do a better job. We have not done a good job the last two outings. We're playing better run defense now than we ever have, so that's a positive. We've got to prepare the same way we prepared last week. We've got to do a better job because if we're not able to stop the run, we're not going to have a chance."