| # | First aired | "The Wørd" | Studio guest | Introductory phrase | Prod#
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| 100 | June 5 | Me | Stone Phillips | None | 2068
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| Stephen celebrates his 100th episode; Stephen looks at how he has changed the world; Stone Phillips becomes the first repeat guest and faces Stephen in a Gravitas-Off rematch. This the first episode in which there is no introductory phrase before the title sequence.
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| 101 | June 6 | Military | Christiane Amanpour | "It's 6-6-6, and this show contains many satanic backmasked messages. tropeR trebloC ehT si sihT." ("This is The Colbert Report" spoken backwards) | 2069
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| Expressed worry about the date, and put holy water, a crucifix, and a copy of the Bible on his shelf. Once the date was nearly over, he replaced them with a stolen shrunken head and an iPod that "plays only a video of the owner's death" and Black Eyed Peas' "My Humps." He then attempted to flip the page on a calendar and received a paper cut.
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| 102 | June 7 | Big Deal | Steve Squyres | "When the world tries to shake us up, I'm America's bubble wrap." | 2070
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| Threat Down: "Ivy Leaguers!" (for cloning through stem cells, thus creating "an army of intellectuals"), "Bad Heroin!", "U.S. Diplomats!" (for offering Iran nuclear technology), "Repetitive Corporate Sponsorships!" (for the Miami Heat's AmericanAirlines Arena vs. the Dallas Mavericks' American Airlines Center), "Conservationists!" (for bringing "Frogs on a Plane"), "and oh, yeah, bears."
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| 103 | June 8 | Gooooaaaaal! | Steven Johnson | "Life is a crap shoot, and I'm your loaded dice." | 2071
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| CInterviewed a videotape of Tom DeLay for the 23rd installment of "Better Know a District." Put his honorary doctorate from Knox College on bookshelf along with pictures of TV doctors Noah Drake from General Hospital, Gregory House from House, and Cliff Huxtable from The Cosby Show. Credits list Producer Dr. Stephen T. Colbert, D.F.A..
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| 104 | June 12 | Tom DeLay's Farewell Speech | Robert F. Kennedy, Jr. | "By the power of Grayskull, this is The Colbert Report." | 2072
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| Colbert places Mort Zuckerman On Notice (replacing "the sea") after U.S. News and World Report sent a fax claiming that he misstated Zuckerman's position on tax cuts. Tip of the Hat, Wag of the Finger: Wag - College Students.
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| 105 | June 13 | Great F**king Idea | Tim Flannery | "This show may be recorded for quality assurance. This... is The Colbert Report." | 2073
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| Apparently nothing happened, or no one remembers?
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| 106 | June 14 | License Renewal | David Sirota | "Loosen your belts, America, I'm gonna force feed you truth like grain down a goose's gullet." | 2074
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| Better Know A District: Lynn Westmoreland (R-GA) from Georgia's 8th; Stephen gives American flags and bibles to the audience and displays a self-waving American flag that also plays patriotic songs.
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| 107 | June 15 | Lock & Load | Michael Pollan | "There's a vicious rumor going around that this is not The Colbert Report, but let me assure you, this is The Colbert Report." | 2075
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| Stephen talks about more applicants for his new black friend, but then reconciles with Alan (and takes a new picture with him); the return of "Formidable Opponent" with detaining suspected terrorists in Guantanamo Bay Naval Base; Stephen adds a Wendy's "Great Biggie" to his bookshelf, as its name was changed to "large."
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| 108 | June 19 | Risky Business | Gustavo Arellano | "I'm going through America's trash separating the white glass of truth from the the green glass of facts." | 2076
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| Stephen releases his new sperm, "Formula 402," in response to the finding that risky actions are caused by genes. The Threat Down, Homo-Sexy Edition: gay superheroes, Cirque de Soleil, the World Cup, the Ex-Gay Movement, desirable men (giving Brad Pitt as an example), and the "other #1 threat," bears.
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| 109 | June 20 | Everything Must Go | Bart Ehrman | "And now, the ten-time winner of the Stephen Colbert Award for Journalistic Excellence, this is The Colbert Ro... Oh shit!" | 2077
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| First installment of "Stephen Makes it Simple," with big government and small government.
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| 110 | June 21 | None | Bay Buchanan | "Today is the summer solstice, the longest day of the year. But what really matters is... how thick is it?" | 2078
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| Alexi Lalas helps Stephen trash talk other teams in the World Cup.
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| 111 | June 22 | Cut and Run | Douglas Brinkley | "This is The Colbert Report, or for our foreign viewers: THIS IS THE COLBERT REPORT!" | 2079
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| Better Know A District: Diana DeGette (D) from Colorado's 1st
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| 112 | June 26 | Class Warfare | Mark Bowden | "Still waiting for my invitation, Nicole and Keith. This is The Colbert Report." | 2080
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| Colbert places a Highlights for Children magazine on his bookshelf in honor of the printing of its one billionth copy.
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| 113 | June 27 | Cold, Dead Fingers | Chris Matthews | "We now return you to The Colbert Report, already in progress." | 2081
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| Movies That Are Destroying America: Stephen recommends that everybody see Strangers with Candy multiple times at full price.
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| 114 | June 28 | Superman | Robert Baer | "I had an acting class this week, and it's really paid off: this is The Colbert Report." | 2082
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| Citizens in Action: Fondue It Yourself. Segment with Cassie Ramoska and Ricky Faust as citizen journalists.
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| 115 | June 29 | Monkey Butter | Christopher Noxon | "Happy Birthday, America. You may be 230, but if you were a dog, you'd only be 32... but you'd be dead 'cause dogs don't live that long. This is The Colbert Report." | 2083
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| Profiled a fireworks salesman in The Difference Makers; said "goodbye" to the Supreme Court; left the show (for the week) in solidarity with Star Jones leaving The View.
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