The "Renix" Fuel Injection System is an older computer system found on Jeeps from 1986 thru 1990. Renix made computers that controlled emission carbuerators used by AMC, Volvo, and Renault (Renault and Bendix started Renix) as well as early Fuel Injection Systems. You'll find the word Renix used to denote these older Jeep Fuel Injection Systems here on Jeep Forum.
Your 1999 Cherokee is an OBDII. It is two (arguable three) generations newer than the Renix. The OBDII systems don't use Exhaust Gas Recirculation (EGR).
EGR is taking some exhaust gas out of the exhaust manifold and feeding into the intake manifold to cool the combustion for emission purposes. Later computers and fuel injection systems no longer needed it to meet the legal emissions requirements.
The older carbeurated and Renix Jeeps had a tube going from the exhaust manifold to the intake manifold to feed the exhaust gas through a valve = EGR. Your 1999 Cherokee did not come with it. Your Dad's friend or the previous owner has put an older, EGR type exhaust manifold on the Cherokee. No biggie if it runs. The late 90s Jeep manifolds are prone to cracking. The Previous Owner (PO) probably got the older manifold cheap and threw it on to replace a cracked one. He had to block or plug the tube for the reason you've discovered. The plug is just a brass plumbing fitting with a bolt and nut down the middle.
A newer, correct, tubing type exhaust manifold is more effecient and will produce more power.