The most common and most likely answer to this crossword clue is the 6 letter word MAYDAY
I've seen this crossword clue in The Guardian
M
A
Y
D
A
Y
More clues leading to the result MAYDAY
- Flying, Amy died, alas - after sending this?
- Ex-PM pitched against ex-political broadcaster – call for help!
- Springtime festival‘s call for help
- Holiday emergency!
- PM, extremely angry about note, makes appeal for help
- Cry for help in publicity about end of democracy welcomed by PM
- Help me to get a holiday
- Home Secretary has support of Sun? We’re in trouble
- When month starts I need help
- Holiday appeal
Buddy explains!

The straight part
We know that "We’re in trouble" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case we’re in trouble = mayday.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does MAYDAY mean?
MAYDAY noun- An international distress signal used by shipping and aircraft