The plan: Ultimecia was a powerful and corrupt sorceress from the future, manipulating events in the present in order to compress all of time into a single moment. This would lead to her absolute dominion over everything, extinguishing as it would, all life but hers. In fact, it would wipe out all existence but her.
The problem: Dominion over everything sounds kind of cool, but the sheen comes off when you consider that “everything” actually translates to “nothing”. And even if Ultimecia was planning on the pulling the old “I will rebuild my own universe” crap, wouldn’t wiping out existence logically mean wiping out whatever universal forces sustained her own magic, rendering the rebuilding of anything impossible?
“Wonewy… I’m so wonewyyy…”
The plan: Given that years of personal confrontations, inter-dimenional weaponry and ninja armies have failed to defeat the Turtles, Shredder throws them through a time portal to be rid of them once and for all, allowing he and Krang to steal the Statue of Liberty in peace.
The problem: We assume that Shredder got his time portal cheap from some Chinese guy on eBay. Not only was it unstable, it actually managed to bring the Turtles back towards the present day roughly every five minutes (co-incidentally just after beating each time zone’s boss).
We’ll say that the temporal energy displacement caused by each battle initiated some sort of Star Trek-style space-time McGuffination, rather than take the lazy angle and cite “VIDEO GAME LOGIC!”, but either way, shoddy work, Saki-san.
And on another note, what the hell is the point of stealing the Statue of Liberty? It provides no useful technology, you can’t exactly sell it inconspicuously, and if the police want to find it they just need to look for the huge metal woman looming 93 metres over the horizon.