Morgan will make his first international start since leading Wales in the World Cup quarter-final defeat against Argentina in October 2023 in Marseille.
The flanker missed the 2024 Six Nations because of a knee problem and the summer tour as a result of a hamstring injury.
Morgan, 24, was named on the bench for the defeat against Fiji but made an impression when he came on in the second half.
Cardiff back row Botham was also prominent in the latter stages last weekend and comes in for Plumtree, who drops out of the 23-man squad, while Reffell is on the bench.
Cardiff wing Grady was ruled out of the autumn series after suffering a first-half injury in the defeat against Fiji, with Rogers preferred to Rio Dyer and Josh Hathaway.
Gatland has opted for the more traditional balance of five forwards and three backs on his bench this time after the tactic of six forwards and two backs backfired against Fiji.
After losing Grady to injury, Gatland admitted afterwards the wrong replacement had been sent on with Scarlets fly-half Sam Costelow playing out of position rather than Cardiff scrum-half Bevan, who had been allocated to cover the wing.
Scarlets centre Eddie James is named as a replacement against Australia.
