The Jr. Jays Magazine followed the adventures of Dr. Jay and his questionable relationships with young characters like Flash, Lambert, Cathy, Ashmede, Ashley, Ronnie, Ben and Crunchie the dog. From what I recall, the comic strip was basically a glorified anti-drug, anti-alcohol, anti-smoking therefore anti-fun PSA which told kids about the values of staying in school and working hard to achieve their dreams.
Over the years, Jr. Jays magazine evolved into what would be known as simply "The Magazine". While no longer focused solely on the Blue Jays, the Jays comic strip continued to run in The Magazine but was eventually phased out after 2000. Actual members of the Toronto Blue Jays occasionally made cameos in the comic strip, with an animated Roberto Alomar as seen below.
Images courtesy of TorontoistUnfortunately, copies of the Jr. Jays magazine are hard to find these days. Apparently there are plans in the works to put the entire series on the internet eventually, but for the time being there is just one copy of the first issue available on eBay.
If someone wants to take one for the team, I'm sure we'd all be more than happy to pitch in and circulate the copy so that everyone gets a chance to relive the memories. In the meantime, check out this video from the very short-lived Jr. Jays TV Magazine on YTV.