England lost six wickets for nine runs in a hapless collapse which turned the first Ashes Test on its head on the second afternoon at the Gabba.
The dismissal of Kevin Pietersen, in his 100th Test, began the damaging sequence of events which left England in disarray on a teatime 94 for eight.
Ryan Harris and Johnson shared the first four wickets, and then off-spinner Lyon took two in two as England lost three stuck on the Australian 'bogey' score of 87.
A variation of recent history was in danger of being repeated when Stuart Broad strode out to face Lyon's hat-trick ball - he was lbw to Peter Siddle here to complete the sequence three years ago - but this time, he was not required to play at an off-break.
There were, conspicuously, no echoes of 2010/11 in the innings of Cook and Trott.
They had batted more than 21 hours between them on their last appearance at this venue, when their twin tour-de-force rearguard laid the first foundations for England's famous series victory three years ago.
This time, after Broad finished with figures of six for 81 and Brad Haddin (94) was run out to end an uneven home innings, they got through barely an hour.
Carberry, back to open at the age of 33 after a solitary previous Test in March 2010, dealt admirably with the initial exchanges.
Cook appeared quietly in control too, until Harris found the perfect line just outside off stump to take a forward-defensive outside edge for caught-behind.
Trott was instantly discomforted as Johnson tested him with the short ball into his body, and Australia's awareness to rush through for an extra over before lunch paid off.
Johnson needed just one more delivery to have Trott edging behind as he tried to get off side of the bounce, but merely deflected the ball into Haddin's gloves.
Johnson duly attacked Pietersen with the short ball too.
But Australia gave up trying to bounce him out, and chose to bore him instead - a tactic which worked when Pietersen clipped to midwicket off Harris, having already escaped a sharp return chance to Siddle.
Johnson then did bounce out Carberry, from round the wicket, as the left-hander fenced a catch to second slip.
But the collapse truly gathered momentum when Bell was caught at short-leg off Lyon, and then Matt Prior went the same way to the very next ball - thanks to DRS, after Aleem Dar had given him not out.
Joe Root was unable to stop the rot, edging compliantly into the slips off Johnson in an England innings which was by now in tatters - and on its last legs by the time Graeme Swann went bat-pad, albeit from a Johnson delivery which should have been called no-ball three minutes before tea.
Broad had to settle for just one more wicket on another sunny morning.
Number 10 Harris began confidently against him, after Australia resumed on 273 for eight.
But with the last ball of his second over, Broad got his man as Harris tried to pull the bat away but instead merely guided a catch behind off the open face.
Haddin tired to nick his hundred while he could but took one risk too many, when he tried to scamper a two into the off side off James Anderson and could not match Carberry's pace and throw.
He had nonetheless served his team well, with a 153-ball rescue act containing eight fours and a six.
As Haddin dashed off the field, having effectively run himself out, Broad followed with ball held aloft - but was predictably greeted by more boos from a crowd determined to dislike him, come what may.
HOW ENGLAND LOST SIX FOR NINE
All was progressing to plan for England an hour after lunch on day two of the Ashes.
But round the corner was a collapse which would turn the first Test on its head at the Gabba.
Here is how six wickets fell for nine runs:
1342 - 82 for three, Kevin Pietersen had come through a barrage of early bouncers from Mitchell Johnson, only to clip Ryan Harris to midwicket for a tame end to his first innings in his 100th Test.
1409 - 87 for four, Michael Carberry's patient vigil foundered on Johnson's pace and bounce from round the wicket as he fended a catch to second slip.
1415 - 87 for five, Ian Bell's was a soft dismissal for a batsman of his undoubted world class as he became the first of Nathan Lyon's victims snaffled at short-leg.
1418 - 87 for six, Matt Prior fell for his second golden duck at this venue in consecutive innings - three years apart. He edged Lyon on to his thigh-pad and into the hands of a jubilant short-leg. Aleem Dar did not detect the edge, but DRS did.
1425 - 89 for seven, Joe Root had no answer to England's troubles, steering an attempted drive into the slips off Johnson.
1435 - 91 for eight, Graeme Swann's departure just before tea - caught bat-pad off Johnson - meant England were struggling even to avoid the follow-on.