Elaborate what you mean by "Plan B". A Plan B for what exactly?
Plan A consists of passing, passing, and passing, onto Messi's feet. When Messi was tired and unfit that night, along with the key people in the passing game, that plan fell apart. Barca also lack a physical presence in set pieces, whilst their defence is relatively untested against heavy weights. They are also over reliant on certain players aside from Messi, when Puyol was missing, or unfit, Pique couldn't help to marshal the start of the attack from the back.
Alves and Alba are great players, but at times they can seem more like wing-backs than fullbacks, leaving them ripped apart by Bayern, who possess excellent wingers.
We can say perhaps that this was all due to injuries and such, but Barca were shown to sorely lack a Plan B when Bayern stacked the midfield, packing in players, with their forwards rushing back, and generally preventing Xavi and Iniesta from working their usual game. Javi Martinez and Schweinsteiger also disrupted the passing game those two nights by committing lots of fouls, which killed off the rhythm that makes Barca's game so deadly. And then, there was nothing on the Bench that could be a Plan B.
One thing that I appreciated late in Arsenal's season was their switch to a Plan B partially. Earlier, their plan was as usual, to play the ''beautiful game'', to score the perfect goal, ''walk the ball into the net'', and the whole host of stereotypes plastered to Arsenal. In the games after Bayern, they switched to a more defensive game plan, grinding out games by scoring early, pressing high, being aggressive and dogged in defence, with Arteta and Ramsey deployed to guard the back four, whilst the forwards (even Walcott!) tracked back sometimes to defend. Lots of 1-0 win margins, but it got the job done when Arsenal were trying to deal with their injury roster, or general ineptitude amongst players.
