Yorvit Torrealba led off the second with a homer, and after loading the bases with an intentional walk to Holliday, who leads the National League in hitting at .349, Vargas walked Todd Helton to bring in another run.
It's rare for a hitter of Helton's stature to find pitchers walking anyone to get to him, but Vargas wasn't surprised at manager Willie Randolph's decision to walk the right-hander and face the lefty.
"Not taking anything away from Helton, but it was left on left," the left-handed Vargas explained. "I made some good pitches to Helton, but I didn't get it done."
Vargas struggled throughout his start, with the Rockies scoring in three of his four innings and getting at least as far as second base in each frame.
"I just wasn't executing pitches when I needed to," Vargas said. "I left a lot of pitches up."
The final straw came in the fourth, when Vargas was removed after again loading the bases with one out, only to watch as reliever Joe Smith served up a grand slam to Ryan Spilborghs.
"When they have a situation where they need a ground-ball double play, they like to use me, and I like to be in that situation," Smith said. "It was a sinker that didn't sink, and he got me."
Three of the runs from the slam went on Vargas' tab -- nine runs, 11 hits, two walks (one intentional), a wild pitch, a balk and two homers.
"He didn't throw the ball well, obviously," said Randolph. "It's tough coming into a situation like that when you need a spot start. You always hope he can give you a boost. He left too many pitches on the plate."
With Perez's spot in the rotation coming up again on Sunday before his expected return following the All-Star break, Randolph and his staff need to decide whether to send Vargas out for another turn that day. Randolph declined to address the issue after the game.
"The results of the game aren't going to change anything," Vargas said. "I'll prepare for my next start the same way I do every other time. I'm just going to be ready for the next time I pitch."
Though Vargas' nine runs put the game out of reach, the three-run output from the Mets was not the kind of run production that encourages confidence in Coors Field games. They seemed to be back on their game in the first inning, with Reyes creating chaos on the basepaths, but the Mets' only other offensive highlight came in the top of the fourth, when Ramon Castro launched his fifth home run, a 402-foot shot into the left-field seats.
Castro's roundtripper was one of the few balls the Mets were able to get airborne against Cook (5-5), who recorded 20 ground-ball outs in his eight innings on the hill.
"He had a good sinker today," said Shawn Green, who accounted for three of Cook's ground-ball outs, including two double plays. "I hit everything right into the ground. I was looking for the sinker away and trying to hit a line drive to left, and there was just late action and I was rolling over it.
"I was thankful there was no one on my third at-bat, or I'd have had three double plays."
Adding a final element of irony, Kazuo Matsui had a career best five hits in the game against his former Mets teammates. They were all singles, including two infield hits. It was the second time a Rockies hitter had five hits in a game this season, both coming against the Mets, with Willy Taveras getting five at Shea Stadium on April 25.
"Great night, 5-for-5," said Reyes of Matsui's performance. "I wish I had a night like that."
Reyes' night was cut short when he was removed as part of a double-switch after the eighth inning, a rare occasion for Reyes not to finish a game he started. He had grounded out to the pitcher, making a less than full effort to run out the play to first with the score already 11-3. But Randolph and Reyes insisted the play had nothing to do with his removal.
"I was just giving him an inning off," Randolph said.
The Mets have had more than their share of "off" innings since arriving in Colorado, being outscored, 17-5, and problems abounding on both sides of the ball.
"Hopefully, we get a chance to win the last game [Wednesday]," Reyes said smiling.