Conversely that same year, WISH-TV lost the ABC affiliation to WTTV; this resulted in WLBC-TV, channel 49 in Muncie (whose allocation is now occupied by PBS member station WIPB) serving as the de facto ABC affiliate for the northern part of the market as WTTV's signal did not extend very far north outside of Indianapolis's northern suburbs as its transmitter was located farther south than the market's other stations.

However, the merger put Belo two stations over the television ownership limits that the Federal Communications Commission had in effect at the time.

LIN was headquartered in Indianapolis for many years, with WISH-TV serving as that company's flagship television property; the company eventually moved its headquarters to Providence, Rhode Island, in the late 1990s, resulting in WPRI-TV replacing WISH as LIN's flagship station.

In 2002, WISH-TV began handling the master control operations of WANE-TV and fellow sister station WLFI-TV in Lafayette, Indiana.

[6] On February 10, 2005, the Paramount Stations Group subsidiary of Viacom sold UPN affiliate WNDY-TV (channel 23, now a MyNetworkTV affiliate) as well as its Columbus, Ohio, sister station WWHO to LIN TV for $85 million, creating a duopoly with WISH-TV when the sale was finalized that spring.

[8] On September 15, 2008, LIN and Time Warner Cable entered into an impasse during negotiations to renew retransmission consent deals for some of the group's television stations.

LIN TV requested compensation for carriage of its stations in a manner similar to the deals that cable networks have with pay television providers, as other broadcast station owners began to seek compensation from cable and satellite providers for their programming.

On August 7, 2009, WISH-TV began operating a Mobile DTV feed of subchannel 8.1, which originally was only accessible via an app for BlackBerry devices.

[11] On January 29, 2010, LIN TV filed an application to the FCC to operate a digital fill-in translator on UHF channel 17,[12] an allotment that was previously occupied by the analog signal of Class A sister station WIIH-CA; the FCC granted a construction permit to build the translator's transmitter facilities on June 16.

As the other major broadcast networks had existing affiliation deals with other area stations (WRTV's ABC affiliation was up for renewal around this time, though the E. W. Scripps Company reached an agreement to allow WRTV and nine of the company's other stations to remain with ABC the day prior to the announcement[19]), WISH announced on December 11, 2014, that it would become an independent station upon losing the CBS affiliation, filling timeslots previously occupied by network shows with additional newscasts and an expanded inventory of syndicated talk shows, newsmagazines, and sitcoms,[20] including some shows relocated from sister station WNDY-TV to make up for the loss of CBS daytime and late-night programs on channel 8's schedule and a national news program from TouchVision (the latter of which was later replaced with an additional half-hour of the station's morning newscast, 24-Hour News 8's Daybreak, on July 13, 2015) to serve as a replacement for the CBS Morning News.

[20][21][22] However, on December 22, 2014, Tribune announced that it would sell the market's CW affiliation to Media General—the deal occurred three days after the completion of the company's merger with LIN.

CBS affiliate WANE-TV in Fort Wayne was the only existing sister station of WISH and WNDY that became part of the combined group, as Media General and Nexstar each sold certain Indiana stations they already owned (Nexstar's Fox affiliate WFFT-TV in Fort Wayne and Media General's two other Indiana-based CBS affiliates, WTHI-TV in Terre Haute and WLFI-TV in Lafayette to Heartland Media, and Nexstar's WEVV-TV in Evansville to Bayou City Broadcasting) to alleviate conflicts with FCC ownership rules.

The move of Colts games to WISH-TV when CBS acquired the rights to the AFC in 1998 coincided with the debut of rookie quarterback Peyton Manning, as well as the station's coverage of the Colts' appearances in Super Bowl XLI (a victory) and Super Bowl XLIV.

The coach's show and Colts Up Close moved to WTTV and its sister Fox affiliate WXIN (channel 59) for the 2015 NFL season.

First on February 17, 2015, WISH signed a two-year agreement with the Indy Eleven to carry home matches from the North American Soccer League team during the 2015 and 2016 seasons; WISH replaced sister station WNDY as the Eleven's local television broadcaster, as that station carried the team's games during its inaugural 2014 season.

The deal for carriage of the games in Indianapolis was required after Tribune Broadcasting discontinued airing sports events involving Chicago-area teams over its WGN America cable channel at the end of 2014.

In 1963, WISH-TV became the first television station in the market to provide extensive live coverage of a major local news event, when it covered the deadly explosion at the Fairgrounds Coliseum.

Debby Knox joined Ahern as co-anchor on the weeknight newscasts in 1980 and remained with the station until she retired on November 26, 2013.

In 1990, WISH-TV implemented the "24-Hour News Source" concept that was originally developed that year by WEWS-TV in Cleveland; the format, which began spreading to other television stations nationwide around that timeframe, involves the production of 30-second news updates that air at or near the top of every hour during local commercial break inserts – even during prime time network and overnight programming – in addition to the station's long-form newscasts in regularly scheduled timeslots.

[51] The 615-composed custom package "A New Wish," introduced on September 5, 2012, was the first theme used by the station in 21 years to omit compositional ties to "Back Home Again in Indiana".

As of June 4, 2018, WISH-TV has returned to using the "In-Sink" news music package containing the "Back Home Again in Indiana" melody.

On February 28, 2005, shortly after LIN TV announced its purchase of channel 23, WISH-TV took over production of WNDY's 10 p.m. newscast from WTHR, which had produced the program from its inception on March 16, 1996; this partnership expanded to include an hour-long extension of WISH's weekday morning newscast at 7 a.m., which debuted on January 5, 2009.